Oxazolidinone compounds and methods of use thereof as antibacterial agents

ABSTRACT

The present invention relates to oxazolidinone compounds of Formula (I): and pharmaceutically acceptable salts thereof, wherein A, E, and R1 are as defined herein. The present invention also relates to compositions which comprise at least one oxazolidinone compound of the invention. The invention also provides methods for inhibiting growth of mycobacterial cells as well as a method of treating mycobacterial infections by  Mycobacterium tuberculosis  comprising administering a therapeutically effective amount of an oxazolidinone of the invention and/or a pharmaceutically acceptable salt thereof, or a composition comprising such compound and/or salt.

FIELD OF THE INVENTION

The present invention relates to novel oxazolidinone compounds useful for the treatment of bacterial infections, particularly mycobacterial infections. The invention also relates to methods of use of oxazolidinone compounds for the treatment of mycobacterial infections such as those caused by Mycobacteria tuberculosis.

BACKGROUND OF THE INVENTION

Mycobacterium is a genus of bacterium, neither truly gram-positive nor truly gram-negative, including pathogens responsible for tuberculosis (M. tuberculosis) and leprosy (M. leprae). Tuberculosis (TB), in particular, despite the availability of anti-TB drugs such as isoniazide and rifampin, is considered to be one of the world's deadliest diseases. According to World Health Organization, in 2012, there were 8.6 million new TB cases and 1.3 million TB deaths. See, Global tuberculosis report 2013 published by the World Health Organization. Complicating the TB epidemic is the rising tide of multi-drug-resistant strains, and the deadly association with HIV. People who are HIV-positive and infected with TB are 30 times more likely to develop active TB than people who are HIV-negative and TB is responsible for the death of one out of every three people with HIV/AIDS worldwide. See, e.g., Kaufmann et al., Trends Microbiol. 1: 2-5 (1993) and Bloom et al., N. Engl. J. Med. 338: 677-678 (1998).

Mycobacteria other than M. tuberculosis are increasingly found in opportunistic infections that plague the AIDS patient. Organisms from the M. avium-intracellulare complex (MAC), especially serotypes four and eight, account for 68% of the mycobacterial isolates from AIDS patients. Enormous numbers of MAC are found (up to 1010 acid-fast bacilli per gram of tissue), and consequently, the prognosis for the infected AIDS patient is poor.

Oxazolidinones are a class of compounds containing 2-oxazolidone, a 5-membered ring containing nitrogen and oxygen, which are used as antimicrobials. See, e.g. WO 2009157423. In general, oxazolidinones are known to be monoamine oxidase inhibitors and to have activity against gram-positive microrganisms. WO 2006022794, Suzuki et al., Med. Chem. Lett. 4:1074-1078 (2013), Yang et al., J. Med. Chem. 58:6389-6409 (2015), Shaw et al., Ann. N.Y. Acad. Sci. 1241:48-70 (2011), Several oxazolidinone antibiotics have been approved or are in clinical trials for the treatment of gram-positive bacterial infections such as methicillin resistant Staphylococcus aureus. Examples of oxazolidinone antibiotics include linezolid (Zyvox™, Pfizer Inc., New York, N.Y.) and tedizolid (Sivextro™, Merck Sharp & Dohme Corp., Kenilworth, N.J.). Tedizolid is used to treat acute bacterial skin and skin structure infections caused by specific susceptible gram-positive bacteria. Linezolid is indicated for the treatment of several infections caused by susceptible strains of gram-positive microorganisms including nosocomial pneumonia, complicated skin and skin structure infections, and community-acquired pneumonia. In addition, it is currently being tested for the treatment of multi-drug resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis (Mtb) in clinical trials. Lee et al., N. Engl. J. Med 367: 1508-18 (2012). Despite clinical efficacy in treating these diseases, long-term use of linezolid has been associated with adverse events including myelosuppression (including anemia and leukopenia) (Hickey et al., Therapy 3(4):521-526 (2006), neuropathy, and serotonin syndrome. These adverse events are hypothesized to be associated with the inhibition of mitochondrial protein synthesis. Flanagan et al., Antimicrobial Agents and Chemotherapy 59(1):178-185 (2015).

Development of oxazolidininone antibiotics that are safer than approved oxazolidinones yet at least as effective would greatly benefit Mtb patients.

SUMMARY OF THE INVENTION

The present invention is directed to certain novel oxazolidinone compounds which have antibacterial activity. The compounds, and their pharmaceutically acceptable salts, can be useful, for example, for the treatment of bacterial infections, for example, mycobacterial infections. More particularly, the present invention includes compounds of Formula I, or a pharmaceutically acceptable salt thereof:

wherein:

R¹ is —CH₂N(R²)₂, —CH₂NR²COR³, —CH₂NR²COOR³, —CH₂NR²CON(R²)₂, —CH₂NR²CONR²N(R²)₂, —CH₂NR²SO₂R³, —CON(R²)₂, —C═NOR³, —CH₂OR⁴, —CH₂NR²R⁴, or —CH₂R⁶;

each occurrence of R² is independently selected from H, C₁-C₆ alkyl, C₂-C₆ alkenyl, and C₃-C₆ cycloalkyl, wherein said C₁-C₆ alkyl, said C₂-C₆ alkenyl, and said C₃-C₆ cycloalkyl can be optionally substituted with up to four substituents, which are independently selected from halogen, —OCH₃, —OH, NH₂, NHCH₃, and N(CH₃)₂;

R³ is H, C₁-C₆ alkyl, C₂-C₆ alkenyl, and C₃-C₆ cycloalkyl, wherein said C₁-C₆ alkyl, said C₂-C₆ alkenyl and said C₃-C₆ cycloalkyl can be optionally substituted with up to four substituents, which are independently selected from halogen, —OCH₃, —OH, NH₂, NHCH₃, and N(CH₃)₂;

R⁴ is a 5- or 6-membered heterocycle, which is optionally substituted with R⁵;

R⁵ is selected from H, halogen, C₁-C₆ alkyl, C₃-C₆ alkenyl, and C₃-C₆ cycloalkyl, wherein said C₁-C₆ alkyl, said C₃-C₆ alkenyl, and said C₃-C₆ cycloalkyl can be optionally substituted with up to four substitutents, which are independently selected from halogen, —OCH₃, —OH, NH₂, NHCH₃, and N(CH₃)₂;

R⁶ is H, C₁-C₆ alkyl, or a 5-membered heterocycle, wherein said 5-membered heterocycle is optionally substituted with up to two R⁷;

R⁷ is H, halogen, oxo, C₁-C₆ alkyl, C₂-C₆ alkenyl, or C₃-C₆ cycloalkyl, wherein said C₁-C₆ alkyl and said C₃-C₆ cycloalkyl can be optionally substituted with from one to four substituents which are independently selected from halogen, OCH₃, OH, NH₂, NHCH₃, and N(CH₃)₂;

E is a 6-membered aryl or a 5- or 6-membered heteroaryl containing from one to three heteratoms independently selected from S, O, and N, wherein said aryl and said heteroaryl are optionally substituted with up to four substituents, which are independently selected from halogen, —CN, —CF₃, —CHF₂, —CH₂NH₂, —CH₂NHCOCH₃, —OCF₃, —OCHF₂, —OH, —O—(C₁-C₆)alkyl, C₁-C₆ alkyl, and C₃-C₆ cycloalkyl;

A is a heterocycle optionally substituted with up to four R⁸, or an aryl substituted with up to four R⁸;

each occurrence of R⁸ is independently selected from halogen, C₁-C₆ alkyl, C₃-C₆ cycloalkyl, C₃-C₆ heterocycloalkyl, benzyl, —OCF₃, —OCHF₂, —OR³, ═O, —CN, —NO₂, —SR³, —SF₅, —SCF₃, —SOR³, —SO₂R³, —S(═O)(═NH)R², —N(R²)₂, —NR²COR³, —SO₂N(R²)₂, —NR²SO₂R³, —COOH, —COR⁹, —COOR³, —CON(R²)₂, and —C(R⁹)₂N(R²)₂, wherein said C₁-C₆ alkyl, C₃-C₆ cycloalkyl, C₃-C₆ heterocycloalkyl, and benzyl are optionally substituted with up to four F, —OCH₃, —OH, ═O, NH₂, NHCH₃, and N(CH₃)₂; and

each occurrence of R⁹ is independently selected from H, C₁-C₆ alkyl, and C₃-C₆ cycloalkyl.

The present invention also relates to a pharmaceutical composition for treating a bacterial infection in a subject, particularly an M. tuberculosis infection, comprising an oxazolidinone compound of the invention and a pharmaceutically acceptable carrier, diluent or excipient.

The Compounds of Formula (I) (also referred to herein as the “Oxazolidinone Compounds”) and pharmaceutically acceptable salts thereof can be useful, for example, for inhibiting the growth of Mycobacterium tuberculosis, and/or for treating or preventing tuberculosis in a patient. Without being bound by any specific theory, it is believed that uses of the Oxazolidinone Compounds of the invention for the treatment of tuberculosis are likely to cause less myelosuppression than known oxazolidinone compounds such as linezolid because they are not associated with a high degree of inhibition of mitochondrial protein synthesis (see Example 65). Additionally, Oxazolidinone Compounds of the invention are more selective than known oxazolidinone compounds, with weaker Gram-positive antibacterial activity and high potency against M. tuberculosis.

The present invention is also directed to 1) methods of treating tuberculosis in a subject in need of treatment thereof, comprising administering to the subject an effective amount of an oxazolidinone compound; and 2) uses of an oxazolidinone compound for the treatment of tuberculosis.

Embodiments, sub-embodiments and features of the present invention are either further described in or will be apparent from the ensuing description, examples and appended claims.

DETAILED DESCRIPTION OF THE INVENTION

Oxazolidinones were originally developed for use in treating gram-positive bacterial infections, particularly, methicillin-resistant S. aureus infections. As shown in the Examples, in vitro testing of the oxazolidinone compounds of Formula I revealed such compounds had excellent potency in inhibiting the growth of Mycobacteria tuberculosis, but did not have strong Gram positive antibacterial activity. Additionally, Oxazolidinone Compounds of the invention are not associated with a high degree of mitochondrial protein synthesis inhibition. Thus, compounds of Formula I and their pharmaceutically acceptable salts are expected to be useful for the treatment of mycobacterial tuberculosis (Mtb), yet not lead to the side effects such as myelosuppression that are associated with with the oxazolidinone linezolid, which is approved for treatment of Gram-positive infections. Therefore, such compounds would have significant advantages over linezolid and analogs as Mtb therapeutic agents.

The Compounds of Formula (I)

In one aspect, the present invention includes compounds of Formula I:

and pharmaceutically acceptable salts thereof, wherein A, E, and R¹ are defined above for the Compounds of Formula (I); wherein the compounds may be suitable for use for the treatment of bacterial infections, particularly mycobacterial infections.

A first embodiment of the invention (Embodiment E1) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein A is an aryl optionally substituted with up to four R⁸; and wherein all other variables are as originally defined (i.e. as defined in Formula I in the Summary of the Invention).

In a sub-embodiment of Embodiment E1, A is a 5-membered aryl. In a further sub-embodiment, A is a 6-membered aryl. In still further sub-embodiments, A is a 7-, 8-, 9-, 10-, 11-, 12-, 13-, or 14-membered aryl.

A second embodiment (Embodiment E2) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is a heteroaryl, wherein from 1 to 4 of the ring atoms is independently O, N, or S and the remaining ring atoms are carbon atoms, and all other variables are as defined in the Summary of the Invention.

In a sub-embodiment of Embodiment E2, A is a 5-membered heteroaryl containing one heteroatom. In a further sub-embodiment, A is a 5-membered heteroaryl containing two heteroatoms. In another sub-embodiment A is a 5-membered heteroaryl containing three heteroatoms. In a still further sub-embodiment A is a 5-membered heteroaryl containing four heteroatoms. In another sub-embodiment, A is a 6-membered heteroaryl containing one heteroatom. In a further sub-embodiment, A is a 6-membered heteroaryl containing two heteroatoms. In another sub-embodiment A is a 6-membered heteroaryl containing three heteroatoms. In a still further sub-embodiment A is a 6-membered heteroaryl containing four heteroatoms. In still further sub-embodiments, A is a 7-, 8-, 9-, 10-, 11-, 12-, 13-, or 14-membered heteroaryl containing from one to four heteroatoms selected from N, O, and S.

A third embodiment (Embodiment E3) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein A is a monocyclic saturated or partially unsaturated ring optionally substituted with up to four R⁸, wherein from 1 to 4 of the ring atoms is independently O, N, or S and the remaining ring atoms are carbon atoms, and all other variables are as defined in the Summary of the Invention.

In a sub-embodiment of Embodiment E3, A is a 5-membered monocyclic saturated or partially unsaturated ring containing one heteroatom. In a further sub-embodiment, A is a 5-membered monocyclic saturated or partially unsaturated ring containing two heteroatoms. In another sub-embodiment A is a 5-membered monocyclic saturated or partially unsaturated ring containing three heteroatoms. In a still further sub-embodiment A is a 5-membered monocyclic saturated or partially unsaturated ring containing four heteroatoms. In another sub-embodiment, A is a 6-membered monocyclic saturated or partially unsaturated ring containing one heteroatom. In a further sub-embodiment, A is a 6-membered monocyclic saturated or partially unsaturated ring containing two heteroatoms. In another sub-embodiment A is a 6-membered monocyclic saturated or partially unsaturated ring containing three heteroatoms. In a still further sub-embodiment A is a 6-membered monocyclic saturated or partially unsaturated ring containing four heteroatoms.

A fourth embodiment (Embodiment E4) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is a bicyclic saturated or partially unsaturated ring system, optionally substituted with up to four R⁸, wherein from 1 to 4 of the ring atoms is independently O, N, or S and the remaining ring atoms are carbon atoms, and all other variables are as defined in the Summary of the Invention.

In a sub-embodiment of Embodiment E4, A is a bicyclic saturated or partially unsaturated ring system containing one heteroatom. In a further sub-embodiment, A is a bicyclic saturated or partially unsaturated ring system containing two heteroatoms. In another sub-embodiment A is a bicyclic saturated or partially unsaturated ring system containing three heteroatoms. In a still further sub-embodiment A is a bicyclic saturated or partially unsaturated ring system containing four heteroatoms.

In Embodiments E1-E4 and sub-embodiments of Embodiments E1-E4, A is optionally substituted with up to four occurrences of R⁸. In sub-embodiments of Embodiments E1-E4 and preceding subembodiments thereof, A is substituted with four occurrences of R⁸, which are as originally defined. In another sub-embodiment, A is substituted with three occurrences of R⁸. In a further sub-embodiment, A is substituted with two occurrences of R⁸. In yet a further sub-embodiment, A is substituted with a single occurrence of R⁸. In alternative embodiments of Embodiments E1-E4, A is unsubstituted.

A fifth embodiment (Embodiment E5) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is selected from the group consisting of:

wherein R⁸ represents up to four optional substituents, which can be the same or different; and

wherein R⁸ and all other variables are as defined in the Summary of the Invention.

In sub-embodiments of Embodiments E5, A is substituted with four occurrences of R⁸. In another sub-embodiment, A is substituted with three occurrences of R⁸. In a further sub-embodiment, A is substituted with two occurrences of R⁸. In yet a further sub-embodiment, A is substituted with a single occurrence of R⁸. In an alternative sub-embodiment of Embodiment E5, A is unsubstituted.

A sixth embodiment (Embodiment E6) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is selected from the group consisting of:

wherein:

m=is 0, 1, 2, or 3;

each occurrence of R⁸ is independently selected from H, halogen, C₁-C₆ alkyl, C₃-C₆ cycloalkyl, C₃-C₆ heterocycloalkyl, benzyl, —OCF₃, —OCHF₂, —OR³, ═O, —CN, —NO₂, —SR³, —SF₅, —SCF₃, —SOR³, —SO₂R³, —S(═O)(═NH)R², —N(R²)₂, —NR²COR³, —SO₂N(R²)₂, —NR²SO₂R³, —COOH, —COR⁹, —COOR³, —CON(R²)₂, and —C(R⁹)₂N(R²)₂, wherein said C₁-C₆ alkyl, C₃-C₆ cycloalkyl, C₃-C₆ heterocycloalkyl, and benzyl are optionally substituted with up to four F, —OCH₃, —OH, ═O, NH₂, NHCH₃, and N(CH₃)₂;

R¹⁰ is selected from H, C₁-C₆ alkyl and C₃-C₆ cycloalkyl, wherein said C₁-C₆ alkyl and said C₃-C₆ cycloalkyl are optionally substituted with from one to four substituents, which are independently selected from F, —OCH₃, —OH, NH₂, NHCH₃, and N(CH₃)₂;

R¹¹ is selected from H, C₁-C₆ alkyl and C₃-C₆ cycloalkyl, —COR⁹, —COOR⁵, —CON(R⁹)₂, and —SO₂R⁹;

each occurrence of R¹² is independently selected from H, halogen, C₁-C₆ alkyl, C₃-C₆ cycloalkyl, benzyl, —OCF₃, —OCHF₂, —OR³, —CN, —NO₂, —SR³, —SF₅, —SCF₃, —SOR³, —SO₂R³, —S(═O)(═NH)R², —N(R²)₂, —NR²COR³, —SO₂N(R²)₂, —NR²SO₂R³, —COOH, —COR⁹, —COOR³, —CON(R²)₂, and —C(R⁹)₂N(R²)₂, wherein said C₁-C₆ alkyl, C₃-C₆ cycloalkyl, and benzyl are optionally substituted with up to four F, —OCH₃, —OH, NH₂, NHCH₃, and N(CH₃)₂;

R¹³ is selected from H, halogen, C₁-C₆ alkyl, C₃-C₆ cycloalkyl, benzyl, —OCF₃, —OCHF₂, —OR³, —CN, —NO₂, —SR³, —SF₅, —SCF₃, —SOR³, —SO₂R³, —S(═O)(═NH)R², —N(R²)₂, —NR²COR³, —SO₂N(R²)₂, —NR²SO₂R³, —COOH, —COR⁹, —COOR³, —CON(R²)₂, and —C(R⁹)₂N(R²)₂, wherein said C₁-C₆ alkyl, C₃-C₆ cycloalkyl, and benzyl are optionally substituted with up to four F, —OCH₃, —OH, NH₂, NHCH₃, and N(CH₃)₂; and

W is selected from O, S, SO, SO₂, and S(═O)(═NH); and

wherein

represents a double or a single bond,

wherein all other variable are as defined in the Summary of the Invention.

In Embodiments E1-E6 and sub-embodiments of Embodiments E1-E6, each occurrence of R⁸ is independently selected from halogen, C₁-C₆ alkyl, C₃-C₆ cycloalkyl, C₃-C₆ heterocycloalkyl, benzyl, —OCF₃, —OCHF₂, —OR³, ═O, —CN, —NO₂, —SR³, —SF₅, —SCF₃, —SOR³, —SO₂R³, —S(═CH₂)C₁-C₆ alkyl, —S(═O)(═NH)R², —N(R²)₂, —NR²COR³, —SO₂N(R²)₂, —NR²SO₂R³, —COOH, —COR⁹, —COOR³, —CON(R²)₂, and —C(R⁹)₂N(R²)₂, wherein said C₁-C₆ alkyl, C₃-C₆ cycloalkyl, C₃-C₆ heterocycloalkyl, and benzyl are optionally substituted with up to four F, —OCH₃, —OH, ═O, NH₂, NHCH₃, and N(CH₃)₂.

In a specific sub-embodiment of Embodiments E1-E6, one or more occurrences of R⁸ is selected from: —H, —OH, —CN, —CH₃, —CH₂NH₂, —CONH₂, C(CH₃)₂OH, —COOC(CH₃)₂CH₃, —SCH₃, —OCH₃, —Cl, —F, —CHF₂, ═O, -cyclopropyl, NO₂, —NHSO₂CH₃, —SO₂N(CH₃)₂, —S(═O)(═NH)CH₃, —SO₂CH₃, —SOCH₃, and —SO₂NH₂.

In another specific sub-embodiment of Embodiments E1-E6, one or more occurrences of R⁸ is selected from:

A seventh embodiment (Embodiment E7) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is a 6-membered aryl, wherein said aryl is optionally substituted with up to four substituents, which are independently selected from halogen, —CN, —CF₃, —CHF₂, —CH₂NH₂, —CH₂NHCOCH₃, —OCF₃, —OCHF₂, —OH, —O—(C₁-C₆)alkyl, C₁-C₆ alkyl, and C₃-C₆ cycloalkyl, and all other variables are as defined in the Summary of the Invention.

An eighth embodiment (Embodiment E8) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is a 5-membered heteroaryl containing from one to three heteratoms independently selected from S, O, and N, wherein said heteroaryl is optionally substituted with up to four substituents, which are independently selected from halogen, —CN, —CF₃, —CHF₂, —CH₂NH₂, —CH₂NHCOCH₃, —OCF₃, —OCHF₂, —OH, —O—(C₁-C₆)alkyl, C₁-C₆ alkyl, and C₃-C₆ cycloalkyl, and all other variables are as defined in the Summary of the Invention.

A ninth embodiment (Embodiment E9) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is a 6--membered heteroaryl containing from one to three heteratoms independently selected from S, O, and N, wherein said aryl is optionally substituted with up to four substituents, which are independently selected from halogen, —CN, —CF₃, —CHF₂, —CH₂NH₂, —CH₂NHCOCH₃, —OCF₃, —OCHF₂, —OH, —O—(C₁-C₆)alkyl, C₁-C₆ alkyl, and C₃-C₆ cycloalkyl, and all other variables are as defined in the Summary of the Invention.

A tenth embodiment (Embodiment E10) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is:

and all other variables are as defined in the Summary of the Invention.

An eleventh embodiment (Embodiment E11) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is:

and all other variables are as defined in the Summary of the Invention.

A twelfth embodiment (Embodiment E12) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the summary of the invention or in any of Embodiments E1-E6, E is:

and all other variables are as originally defined.

A thirteenth embodiment (Embodiment E13) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiments E7-E12, and R¹ is selected from —CH₂N(R²)₂, —CH₂NR²COR³, —CH₂NR²COOR³, —CH₂NR²CON(R²)₂, —CH₂NR²CONR²N(R²)₂, —CH₂NSO₂R³, —CON(R²)₂, —C═NOR³, —CH₂OR⁴, —CH₂NR²R⁴, and —CH₂R⁶.

A fourteenth embodiment (Embodiment E14) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E12, and R¹ is —CH₂N(R²)₂.

In a sub-embodiment of Embodiment E14, one occurrence of R² is H and one occurrence of R² is C₁-C₆ alkyl, wherein said C₁-C₆ alkyl is optionally substituted with up to four substitutents, which are independently selected from halogen, —OCH₃, —OH, —NH₂, —NHCH₃, and —N(CH₃)₂.

In a further sub-embodiment of Embodiment E14, one occurrence of R² is H and one occurrence of R² is C₂-C₆ alkenyl, wherein said C₂-C₆ alkenyl is optionally substituted with up to four substitutents, which are independently selected from halogen, —OCH₃, —OH, —NH₂, —NHCH₃, and —N(CH₃)₂.

In a still further sub-embodiment of Embodiment E14, one occurrence of R² is H and one occurrence of R² is C₃-C₆ cycloalkyl, wherein said C₃-C₆ cycloalkyl is optionally substituted with up to four substitutents, which are independently selected from halogen, —OCH₃, —OH, —NH₂, —NHCH₃, and —N(CH₃)₂.

A fifteenth embodiment (Embodiment E15) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiments E7-E12, and R¹ is —CH₂NR²COR³

A sixteenth embodiment (Embodiment E16) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiments E7-E12, and R¹ is —CH₂NR²COOR³.

An seventeenth embodiment (Embodiment E17) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiments E7-E12, and R¹ is —CH₂NR²CON(R²)₂.

In a sub-embodiment of Embodiment E17, R¹ is —CH₂NHCON(R²)₂.

In a further sub-embodiment, R¹ is —CH₂NR²CONH(R²).

In another sub-embodiment, R¹ is —CH₂NR²CONH₂.

A eighteenth embodiment (Embodiment E18) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E12, and R¹ is —CH₂NR²CONR²N(R²)₂.

In a sub-embodiment of Embodiment E18, R¹ is —CH₂NHCONR²N(R²)₂.

In a sub-embodiment of Embodiment E18, R¹ is —CH₂NR²CONHN(R²)₂.

In another sub-embodiment of Embodiment E18, R¹ is —CH₂NR²CONR²NH(R²).

In a further sub-embodiment of Embodiment E18, R¹ is —CH₂NHCONHN(R²)₂.

In a sub-embodiment of Embodiment E18, R¹ is —CH₂NR²CONR²NH₂.

In a sub-embodiment of Embodiment E18, R¹ is —CH₂NR²CONHNH₂.

In a sub-embodiment of Embodiment E18, R¹ is —CH₂NHCONR²NH₂.

A nineteenth embodiment (Embodiment E19) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E12, and R¹ is —CH₂NR²SO₂R³.

A twentieth embodiment (Embodiment E20) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E12, and R¹ is —CON(R²)₂.

In a sub-embodiment of Embodiment E20, one occurrence of R² is H and one occurrence of R² is C₁-C₆ alkyl, wherein said C₁-C₆ alkyl is optionally substituted with up to four substitutents, which are independently selected from halogen, —OCH₃, —OH, —NH₂, —NHCH₃, and —N(CH₃)₂.

In a further sub-embodiment of Embodiment E20, one occurrence of R² is H and one occurrence of R² is C₂-C₆ alkenyl, wherein said C₂-C₆ alkenyl is optionally substituted with up to four substitutents, which are independently selected from halogen, —OCH₃, —OH, —NH₂, —NHCH₃, and —N(CH₃)₂.

In a still further sub-embodiment of Embodiment E20, one occurrence of R² is H and one occurrence of R² is C₃-C₆ cycloalkyl, wherein said C₃-C₆ cycloalkyl is optionally substituted with up to four substitutents, which are independently selected from halogen, —OCH₃, —OH, —NH₂, —NHCH₃, and —N(CH₃)₂.

A twenty-first embodiment (Embodiment E21) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E12, and R¹ is —C═NOR³.

In sub-embodiments of Embodiments E15, E16, E19, and E21, R³ is H

In sub-embodiments of Embodiments E15, E16, E19, and E21, R³ is C₁-C₆ alkyl, wherein said C₁-C₆ alkyl can be optionally substituted with up to four substituents, which are independently selected from halogen, —OCH₃, —OH, —NH₂, —NHCH₃, and —N(CH₃)₂.

In sub-embodiments of Embodiments E15, E16, E19, and E21, R³ is C₂-C₆ alkenyl, wherein said C₂-C₆ alkenyl can be optionally substituted with up to four substituents, which are independently selected from halogen, —OCH₃, —OH, —NH₂, —NHCH₃, and —N(CH₃)₂.

In sub-embodiments of Embodiments E15, E16, E19, and E21, R³ is C₃-C₆ cycloalkyl, wherein said C₃-C₆ cycloalkyl can be optionally substituted with up to four substituents, which are independently selected from halogen, —OCH₃, —OH, —NH₂, —NHCH₃, and —N(CH₃)₂.

A twenty-second embodiment (Embodiment E22) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E12, and R¹ is —CH₂OR⁴.

A twenty-third embodiment (Embodiment E23) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E12, and R¹ is —CH₂NR²R⁴.

In sub-embodiments of Embodiments E22 and E23, R⁴ is a 5-membered heterocycle, optionally substituted with R⁵.

In sub-embodiments of Embodiments E22 and E23, R⁴ is a 6-membered heterocycle, optionally substituted with R⁵.

In sub-embodiments of Embodiments E15, E16, E19, and E23, R² is H.

In further sub-embodiments of Embodiments E15, E16, E19, and E23, R² is C₁-C₆ alkyl, wherein said C₁-C₆ alkyl is optionally substituted with up to four substituents, which are independently selected from halogen, —OCH₃, —OH, NH₂, NHCH₃, and N(CH₃)₂.

In other sub-embodiments of Embodiments E15, E16, E19, and E23, R² is C₂-C₆ alkenyl, wherein said C₂-C₆ alkenyl is optionally substituted with up to four substituents, which are independently selected from halogen, —OCH₃, —OH, NH₂, NHCH₃, and N(CH₃)₂.

In alternate sub-embodiments of Embodiments E15, E16, E19, and E23, R² is C₃-C₆ cycloalkyl, wherein said C₃-C₆ cycloalkyl is optionally substituted with up to four substituents, which are independently selected from halogen, —OCH₃, —OH, NH₂, NHCH₃, and N(CH₃)₂.

A twenty-fourth embodiment (Embodiment E24) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E12, and R¹ is —CH₂R⁶.

In a sub-embodiment of Embodiment E24, R⁶ is H.

In a sub-embodiment of Embodiment E24, R⁶ is C₁-C₆ alkyl.

In a sub-embodiment of Embodiment E24, R⁶ is a 5-membered heterocycle, wherein said 5-membered heterocycle is optionally substituted with one or two R⁷.

A twenty-fifth embodiment (Embodiment E25) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is defined in any of Embodiments E7-E12, and R¹ is —CH₂NH₂.

A twenty-sixth embodiment (Embodiment E26) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E12, and R¹ is —CH₂NHC(O)CH₃.

A twenty-seventh embodiment (Embodiment E27) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E12, and R¹ is —CH₂NHC(O)-cyclopropyl.

A twenty-eighth embodiment (Embodiment E28) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E12, and R¹ is —CH₂NHCOOCH₃.

A twenty-ninth embodiment (Embodiment E29) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E12, and R¹ is —CH₂NHCOCH₂NH₂.

A thirtieth embodiment (Embodiment E30) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E12, and R¹ is CH₂NHCOCHCH₂CH₃.

A thirty-first embodiment (Embodiment E31) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E12, and R¹ is CH₂NHC(O)NHN(CH₃)₂.

A thirty-second embodiment (Embodiment E32) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E12, and R¹ is:

A thirty-third embodiment (Embodiment E33) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E13, and R¹ is:

A thirty-fourth embodiment (Embodiment E34) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E13, and R¹ is:

A thirty-fifth embodiment (Embodiment E35) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E13, and R¹ is:

A thirty-sixth embodiment (Embodiment E36) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E13, and R¹ is:

A thirty-seventh embodiment (Embodiment E37) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein, A is as defined in the Summary of the Invention or in any of Embodiments E1-E6, E is as defined in any of Embodiment E7-E13, and R¹ is:

A thirty-eighth embodiment (Embodiment E38) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein A is as defined in any of Embodiments E1-E6, E is defined in any of Embodiments E7-E12, R¹ is —CH₂OR⁴ or —CH₂NR²R⁴; and

R⁴ is selected from:

A thirty-ninth embodiment (Embodiment E39) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein A is as defined in any of Embodiments E1-E6, E is defined in any of Embodiments E7-E12, R¹ is CH₂R⁶ and R⁶ is selected from:

A fortieth embodiment (Embodiment E40) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein A is:

wherein R⁸ represents up to four optional ring carbon substituents, which can be the same or different, E is defined in any of Embodiments E7-E12, and R¹ is defined in any of Embodiments E13-E37.

A forty-first embodiment (Embodiment E41) is a compound of Formula I, or a pharmaceutically acceptable salt thereof, wherein E is as defined in any of Embodiments E7-E12, R¹ is defined in any of Embodiments E13-E37, A is:

wherein:

m=is 0, 1, 2, or 3;

each occurrence of R⁸ is independently selected from H, halogen, C₁-C₆ alkyl, C₃-C₆ cycloalkyl, C₃-C₆ heterocycloalkyl, benzyl, —OCF₃, —OCHF₂, —OR³, ═O, —CN, —NO₂, —SR³, —SF₅, —SCF₃, —SOR³, —SO₂R³, —S(═O)(═NH)R², —N(R²)₂, —NR²COR³, —SO₂N(R²)₂, —NR²SO₂R³, —COOH, —COR⁹, —COOR³, —CON(R²)₂, and —C(R⁹)₂N(R²)₂, wherein said C₁-C₆ alkyl, C₃-C₆ cycloalkyl, C₃-C₆ heterocycloalkyl, and benzyl are optionally substituted with up to four F, —OCH₃, —OH, ═O, NH₂, NHCH₃, and N(CH₃)₂;

R¹⁰ is selected from H, C₁-C₆ alkyl and C₃-C₆ cycloalkyl, wherein said C₁-C₆ alkyl and said C₃-C₆ cycloalkyl are optionally substituted with from one to four substituents, which are independently selected from F, —OCH₃, —OH, NH₂, NHCH₃, and N(CH₃)₂;

R¹¹ is selected from H, C₁-C₆ alkyl and C₃-C₆ cycloalkyl, —COR⁹, —COOR⁵, —CON(R⁹)₂, and —SO₂R⁹;

each occurrence of R¹² is independently selected from H, halogen, C₁-C₆ alkyl, C₃-C₆ cycloalkyl, benzyl, —OCF₃, —OCHF₂, —OR³, —CN, —NO₂, —SR³, —SF₅, —SCF₃, —SOR³, —SO₂R³, —S(═O)(═NH)R², —N(R²)₂, —NR²COR³, —SO₂N(R²)₂, —NR²SO₂R³, —COOH, —COR⁹, —COOR³, —CON(R²)₂, and —C(R⁹)₂N(R²)₂, wherein said C₁-C₆ alkyl, C₃-C₆ cycloalkyl, and benzyl are optionally substituted with up to four F, —OCH₃, —OH, NH₂, NHCH₃, and N(CH₃)₂;

R¹³ is selected from H, halogen, C₁-C₆ alkyl, C₃-C₆ cycloalkyl, benzyl, —OCF₃, —OCHF₂, —OR³, —CN, —NO₂, —SR³, —SF₅, —SCF₃, —SOR³, —SO₂R³, —S(═O)(═NH)R², —N(R²)₂, —NR²COR³, —SO₂N(R²)₂, —NR²SO₂R³, —COOH, —COR⁹, —COOR³, —CON(R²)₂, and —C(R⁹)₂N(R²)₂, wherein said C₁-C₆ alkyl, C₃-C₆ cycloalkyl, and benzyl are optionally substituted with up to four F, —OCH₃, —OH, NH₂, NHCH₃, and N(CH₃)₂; and

W is selected from O, S, SO, SO₂, and S(═O)(═NH); and

wherein

represents a double or a single bond and wherein all other variables are as defined in the Summary of the Invention.

A forty-second embodiment (Embodiment E42) is a compound of Formula IA, or a pharmaceutically acceptable salt thereof, having the formula:

wherein:

-   -   R¹ is —CH₂NH₂, —CH₂NHC(O)CH₃, —CH₂NHC(O)—C₃-C₆cycloalkyl, or         CH₂R⁶; A is as defined in any of Embodiments E1-E6; and R⁶ is as         defined in the Summary of the Invention.

A forty-third embodiment (Embodiment E43) is a compound of Formula IB, or a pharmaceutically acceptable salt thereof, having the formula:

wherein:

-   -   R¹ is —CH₂NH₂, —CH₂NHC(O)CH₃, —CH₂NHC(O)—C₃-C₆cycloalkyl, or         CH₂R⁶; A is as defined in any of Embodiments E1-E6; and R⁶ is as         defined in the Summary of the Invention.

In sub-embodiments of Embodiments E42 and E43, R¹ is —CH₂NH₂.

In additional sub-embodiments of Embodiments E42 and E43, A is:

wherein R8 represents up to four optional ring carbon substituents, which can be the same or different.

Reference to different embodiments with respect to Formula I compounds, specifically includes different embodiments of Formula I such as Formula IA and Formula IB, sub-embodiments of Formula IA and Formula IB, other embodiments provided herein, and individual compounds described herein.

Other embodiments of the present invention include the following:

(a) A pharmaceutical composition comprising an effective amount of a compound of Formula I, IA, or IB, as defined herein, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.

(b) The pharmaceutical composition of (a), further comprising a second compound, wherein the second compound is an antibiotic.

(c) The pharmaceutical composition of (b), wherein the second compound is selected from the group consisting of: ethambutol, pyrazinamide, isoniazid, levofloxacin, moxifloxacin, gatifloxacin, ofloxacin, kanamycin, amikacin, capreomycin, streptomycin, ethionamide, prothionamide, cycloserine, terididone, para-aminosalicylic acid, clofazimine, clarithromycin, amoxicillin-clavulanate, thiacetazone, meropenem-clavulanate, and thioridazine.

(d) A pharmaceutical composition comprising (i) a compound of formula I, IA, or IB, or a pharmaceutically acceptable salt thereof, and (ii) a second compound, wherein the second compound is an antibiotic, wherein the compound of formula I, IA, or IB, and the second compound are each employed in an amount that renders the combination effective for treating or preventing bacterial infection.

(e) The combination of (d), wherein the second compound is selected from the group consisting of: ethambutol, pyrazinamide, isoniazid, levofloxacin, moxifloxacin, gatifloxacin, ofloxacin, kanamycin, amikacin, capreomycin, streptomycin, ethionamide, prothionamide, cycloserine, terididone, para-aminosalicylic acid, clofazimine, clarithromycin, amoxicillin-clavulanate, thiacetazone, meropenem-clavulanate, and thioridazine.

(f) A method for treating a bacterial infection in a subject which comprises administering to a subject in need of such treatment an effective amount of a compound of Formula I, Ia, or Ib, or a pharmaceutically acceptable salt thereof.

(g) A method for preventing and/or treating a bacterial infection which comprises administering to a subject in need of such treatment an effective amount of a compound of Formula I, Ia, or Ib, or a pharmaceutically acceptable salt thereof.

(h) A method for treating a bacterial infection which comprises administering to a subject in need of such treatment a therapeutically effective amount of the composition of (a), (b), (c), (d), or (e).

(i) The method of treating a bacterial infection as set forth in (f), (g), or (h), wherein the bacterial infection is due to Mycobacterium tuberculosis.

(j) A method for preventing and/or treating a mycobacterial infection which comprises administering to a subject in need of such treatment an effective amount of a composition comprising an oxazolidinone compound, or a pharmaceutically acceptable salt thereof.

(k) The method of treating a mycobacterial infection as set forth in (j), wherein the mycobacterial infection is due to M. tuberculosis.

(l) The method of treating a mycobacterial infection as set forth in (j), wherein the composition is a composition of (a), (b), (c), (d), or (e).

The present invention also includes a compound of Formula I, Ia, or Ib, or a pharmaceutically acceptable salt thereof, (i) for use in, (ii) for use as a medicament for, or (iii) for use in the preparation (or manufacture) of a medicament for, medicine or treating bacterial infection, particularly a mycobacterial infection. In these uses, the compounds of the present invention can optionally be employed in combination with one or more second therapeutic agents including ethambutol, pyrazinamide, isoniazid, levofloxacin, moxifloxacin, gatifloxacin, ofloxacin, kanamycin, amikacin, capreomycin, streptomycin, ethionamide, prothionamide, cycloserine, terididone, para-aminosalicylic acid, clofazimine, clarithromycin, amoxicillin-clavulanate, thiacetazone, meropenem-clavulanate, and thioridazine.

Additional embodiments of the invention include the pharmaceutical compositions, combinations and methods set forth in (a)-(l) above and the uses set forth in the preceding paragraph, wherein the compound of the present invention employed therein is a compound of one of the embodiments, sub-embodiments, classes or sub-classes described above. The compound may optionally be used in the form of a pharmaceutically acceptable salt in these embodiments.

In the embodiments of the compounds and salts provided above, it is to be understood that each embodiment may be combined with one or more other embodiments, to the extent that such a combination provides a stable compound or salt and is consistent with the description of the embodiments. It is further to be understood that the embodiments of compositions and methods provided as (a) through (1) above are understood to include all embodiments of the compounds and/or salts, including such embodiments as result from combinations of embodiments.

Additional embodiments of the present invention include each of the pharmaceutical compositions, combinations, methods and uses set forth in the preceding paragraphs, wherein the compound of the present invention or its salt employed therein is substantially pure. With respect to a pharmaceutical composition comprising a compound of Formula I, IA, or IB or its salt and a pharmaceutically acceptable carrier and optionally one or more excipients, it is understood that the term “substantially pure” is in reference to a compound of Formula I, IA, or IB or its salt per se; i.e., the purity of the active ingredient in the composition.

Definitions and Abbreviations

The terms used herein have their ordinary meaning and the meaning of such terms is independent at each occurrence thereof. That notwithstanding and except where stated otherwise, the following definitions apply throughout the specification and claims. Chemical names, common names, and chemical structures may be used interchangeably to describe the same structure. If a chemical compound is referred to using both a chemical structure and a chemical name and an ambiguity exists between the structure and the name, the structure predominates. These definitions apply regardless of whether a term is used by itself or in combination with other terms, unless otherwise indicated. Hence, the definition of “alkyl” applies to “alkyl” as well as the “alkyl” portions of “hydroxyalkyl,” “haloalkyl,” “—O-alkyl,” etc. . . . .

As used herein, and throughout this disclosure, the following terms, unless otherwise indicated, shall be understood to have the following meanings:

“Alkyl” means saturated carbon chains which may be linear or branched or combinations thereof, unless the carbon chain is defined otherwise. Other groups having the prefix “alk”, such as alkoxy and alkanoyl, also may be linear or branched, or combinations thereof, unless the carbon chain is defined otherwise. Examples of alkyl groups include methyl, ethyl, propyl, isopropyl, butyl, sec- and tert-butyl, pentyl, hexyl, heptyl, octyl, and the like.

“Alkenyl” means carbon chains which contain at least one carbon-carbon double bond, and which may be linear or branched, or combinations thereof, unless otherwise defined. Examples of alkenyl include vinyl, allyl, isopropenyl, pentenyl, hexenyl, heptenyl, 1-propenyl, 2-butenyl, 2-methyl-2-butenyl, and the like.

“Antibiotic” refers to a compound or composition which decreases the viability of a microorganism, or which inhibits the growth or proliferation of a microorganism. The phrase “inhibits the growth or proliferation” means increasing the generation time (i.e., the time required for the bacterial cell to divide or for the population to double) by at least about 2-fold. Preferred antibiotics are those which can increase the generation time by at least about 10-fold or more (e.g., at least about 100-fold or even indefinitely, as in total cell death). As used in this disclosure, an antibiotic is further intended to include an antimicrobial, bacteriostatic, or bactericidal agent.

“About”, when modifying the quantity (e.g., kg, L, or equivalents) of a substance or composition, or the value of a physical property, or the value of a parameter characterizing a process step (e.g., the temperature at which a process step is conducted), or the like refers to variation in the numerical quantity that can occur, for example, through typical measuring, handling and sampling procedures involved in the preparation, characterization and/or use of the substance or composition; through inadvertent error in these procedures; through differences in the manufacture, source, or purity of the ingredients employed to make or use the compositions or carry out the procedures; and the like. In certain embodiments, “about” can mean a variation of ±0.1, 0.2, 0.3, 0.4, 0.5, 1.0, 2.0, 3.0, 4.0, or 5.0 of the appropriate unit. In certain embodiments, “about” can mean a variation of ±1%, 2%, 3%, 4%, 5%, 10%, or 20%.

“Aromatic ring system” means monocyclic, bicyclic or tricyclic aromatic ring or ring system containing 5-14 ring atoms, wherein at least one of the rings is aromatic. Aromatic ring systems, as used herein, encompass aryls and heteroaryls. The term may be used to describe a carbocyclic ring fused to an aryl group. For example, a 5-7-membered cycloalkyl can be fused through two adjacent ring atoms to a 5-6-membered heteroaryl containing 1, 2, or 3 heteroatom ring atoms selected from N, O, and S. In another example, a heteromonocyclic ring is fused through two ring atoms to a phenyl or 5-6-membered heteroaryl containing 1, 2, or 3 heteroatoms selected from N, O, and S.

“Aryl” means a monocyclic, bicyclic or tricyclic carbocyclic aromatic ring or ring system containing 5-14 carbon atoms, wherein at least one of the rings is aromatic. Examples of aryl include phenyl and naphthyl.

“Cycloalkyl” means a saturated monocyclic, bicyclic or bridged carbocyclic ring, having a specified number of carbon atoms. Examples of cycloalkyl include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and the like.

The term “heterocycloalkyl,” as used herein, refers to a non-aromatic saturated monocyclic or multicyclic ring system comprising 3 to 11 ring atoms, wherein from 1 to 4 of the ring atoms are independently O, S, or N, and the remainder of the ring atoms are carbon atoms. A heterocycloalkyl group can be joined via a ring carbon or ring nitrogen atom (if present). In one embodiment, a heterocycloalkyl group is monocyclic and has from about 3 to about 7 ring atoms. In another embodiment, a heterocycloalkyl group is monocyclic has from about 4 to about 7 ring atoms. In another embodiment, a heterocycloalkyl group is bicyclic and has from about 7 to about 11 ring atoms. In still another embodiment, a heterocycloalkyl group is monocyclic and has 5 or 6 ring atoms. In one embodiment, a heterocycloalkyl group is monocyclic. In another embodiment, a heterocycloalkyl group is bicyclic. There are no adjacent oxygen and/or sulfur atoms present in the ring system. Any —NH group in a heterocycloalkyl ring may exist protected such as, for example, as an —N(BOC), —N(Cbz), —N(Tos) group and the like; such protected heterocycloalkyl groups are considered part of this invention. The term “heterocycloalkyl” also encompasses a heterocycloalkyl group, as defined above, which is fused to an aryl (e.g., benzene) or heteroaryl ring. A heterocycloalkyl group can be optionally substituted by one or more “ring system substituents” which may be the same or different, and are as defined herein below. The nitrogen or sulfur atom of the heterocycloalkyl (if present) can be optionally oxidized to the corresponding N-oxide, S-oxide or S,S-dioxide. Non-limiting examples of monocyclic heterocycloalkyl rings include oxetanyl, piperidyl, pyrrolidinyl, piperazinyl, morpholinyl, thiomorpholinyl, thiazolidinyl, 1,4-dioxanyl, tetrahydrofuranyl, tetrahydrothiophenyl, delta-lactam, delta-lactone, silacyclopentane, silapyrrolidine and the like, and all isomers thereof.

As used herein, e.g. in the definition of R¹, “—CH₂NR²COR³” means “—CH₂NR²C═OR³”.

“Drug resistant” means, in connection with a Mycobacterium, a Mycobacterium which is no longer susceptible to at least one previously effective drug; which has developed the ability to withstand antibiotic attack by at least one previously effective drug. A drug resistant strain may relay that ability to withstand to its progeny. Said resistance may be due to random genetic mutations in the bacterial cell that alters its sensitivity to a single drug or to different drugs.

“Halogen” includes fluorine, chlorine, bromine and iodine.

“Heteroaryl”, as used herein, refers to an monocyclic or multicyclic ring system comprising about 5 to about 14 ring atoms, wherein from 1 to 4 of the ring atoms is independently O, N, or S and the remaining ring atoms are carbon atoms, wherein at least one of the heteroatom containing rings is aromatic. In one embodiment, a heteroaryl group has 5 to 10 ring atoms. In another embodiment, a heteroaryl group is monocyclic and has 5 or 6 ring atoms. In another embodiment, a heteroaryl group is bicyclic. A heteroaryl group can be optionally substituted by one or more “ring system substituents” which may be the same or different, and are as defined herein below. A heteroaryl group is joined via a ring carbon atom, and any nitrogen atom of a heteroaryl can be optionally oxidized to the corresponding N-oxide. The term “heteroaryl” also encompasses a heteroaryl group, as defined above, which is fused to a benzene ring. Non-limiting examples of heteroaryls include pyridyl, pyrazinyl, furanyl, thienyl, pyrimidinyl, pyridone (including N-substituted pyridones), isoxazolyl, isothiazolyl, oxazolyl, oxadiazolyl, thiazolyl, pyrazolyl, furazanyl, pyrrolyl, triazolyl, 1,2,4-thiadiazolyl, pyrazinyl, pyridazinyl, quinoxalinyl, phthalazinyl, oxindolyl, imidazo[1,2-a]pyridinyl, imidazo[2,1-b]thiazolyl, benzofurazanyl, indolyl, azaindolyl, benzimidazolyl, benzothienyl, quinolinyl, imidazolyl, benzimidazolyl, thienopyridyl, quinazolinyl, thienopyrimidyl, pyrrolopyridyl, imidazopyridyl, isoquinolinyl, benzoazaindolyl, 1,2,4-triazinyl, benzothiazolyl and the like, and all isomeric forms thereof. In another embodiment of the present invention, heteroaryl is pyridine. Examples of bicyclic rings include:

“Heterocycle” means a monocyclic or bicyclic saturated, partially unsaturated, or unsaturated ring system containing 5-10 atoms and containing at least one ring heteroatom selected from N, S and O. In select embodiments, the ring system contains 1-4 heteroatoms selected from N, S and O. When a heterocycle contains two rings, the rings may be fused, bridged or spirocyclic. Examples of monocyclic heterocycle rings include piperazine, piperidine, and morpholine. Examples of bicyclic heterocycle rings include 1,4-diazabicyclo[2,2,2]octane and 2,6-diazaspiroheptane.

“Oxo” means an oxygen atom connected to another atom by a double bond and is can be represented “=0”.

“Tuberculosis” comprises disease states usually associated with infections caused by mycobacteria species comprising M. tuberculosis complex. The term “tuberculosis” is also associated with mycobacterial infections caused by mycobacteria other than M. tuberculosis (MOTT). Other mycobacterial species include M. avium-intracellulare, M. kansarii, M. fortuitum, M. chelonae, M. leprae, M. africanum, and M. micron, M. avium paratuberculosis, M intracellulare, M. scrofulaceum, M. xenopi, M. marinum, and M. ulcerans.

Another embodiment of the present invention is a compound of Formula I, or a pharmaceutically acceptable salt thereof, as originally defined or as defined in any of the foregoing embodiments, sub-embodiments, aspects, classes or sub-classes, wherein the compound or its salt is in a substantially pure form. As used herein “substantially pure” means suitably at least about 60 wt. %, typically at least about 70 wt. %, preferably at least about 80 wt. %, more preferably at least about 90 wt. % (e.g., from about 90 wt. % to about 99 wt. %), even more preferably at least about 95 wt. % (e.g., from about 95 wt. % to about 99 wt. %, or from about 98 wt. % to 100 wt. %), and most preferably at least about 99 wt. % (e.g., 100 wt. %) of a product containing a compound of Formula I, IA, or IB or a salt of Formula I, IA, or IB (e.g., the product isolated from a reaction mixture affording the compound or salt) consists of the compound or salt. The level of purity of the compounds and salts can be determined using a standard method of analysis such as thin layer chromatography, gel electrophoresis, high performance liquid chromatography, and/or mass spectrometry. If more than one method of analysis is employed and the methods provide experimentally significant differences in the level of purity determined, then the method providing the highest level of purity governs. A compound or salt of 100% purity is one which is free of detectable impurities as determined by a standard method of analysis. With respect to a compound of the invention which has one or more asymmetric centers and can occur as mixtures of stereoisomers, a substantially pure compound can be either a substantially pure mixture of the stereoisomers or a substantially pure individual diastereomer or enantiomer.

The present invention encompasses all stereoisomeric forms of the compounds of Formula I, Formula IA and Formula IB. Unless a specific stereochemistry is indicated, the present invention is meant to comprehend all such isomeric forms of these compounds. Centers of asymmetry that are present in the compounds of Formula I, Formula IA, and Formula IB can all independently of one another have (R) configuration or (S) configuration. When bonds to the chiral carbon are depicted as straight lines in the structural Formulas of the invention, it is understood that both the (R) and (S) configurations of the chiral carbon, and hence both enantiomers and mixtures thereof, are embraced within the Formula. Similarly, when a compound name is recited without a chiral designation for a chiral carbon, it is understood that both the (R) and (S) configurations of the chiral carbon, and hence individual enantiomers and mixtures thereof, are embraced by the name. The production of specific stereoisomers or mixtures thereof may be identified in the Examples where such stereoisomers or mixtures were obtained, but this in no way limits the inclusion of all stereoisomers and mixtures thereof from being within the scope of this invention.

The invention includes all possible enantiomers and diastereomers and mixtures of two or more stereoisomers, for example mixtures of enantiomers and/or diastereomers, in all ratios. Thus, enantiomers are a subject of the invention in enantiomerically pure form, both as levorotatory and as dextrorotatory antipodes, in the form of racemates and in the form of mixtures of the two enantiomers in all ratios. In the case of a cis/trans isomerism the invention includes both the cis form and the trans form as well as mixtures of these forms in all ratios. The preparation of individual stereoisomers can be carried out, if desired, by separation of a mixture by customary methods, for example by chromatography or crystallization, by the use of stereochemically uniform starting materials for the synthesis or by stereoselective synthesis. Optionally a derivatization can be carried out before a separation of stereoisomers. The separation of a mixture of stereoisomers can be carried out at an intermediate step during the synthesis of a compound of Formula I, Formula IA, or Formula IB or it can be done on a final racemic product. Absolute stereochemistry may be determined by X-ray crystallography of crystalline products or crystalline intermediates which are derivatized, if necessary, with a reagent containing a stereogenic center of known configuration. Where compounds of this invention are capable of tautomerization, all individual tautomers as well as mixtures thereof are included in the scope of this invention. Unless a particular isomer, salt, solvate (including hydrates) or solvated salt of such racemate, enantiomer, diastereomer or tautomer is indicated, the present invention includes all such isomers, as well as salts, solvates (including hydrates) and solvated salts of such racemates, enantiomers, diastereomers and tautomers and mixtures thereof.

When any variable (e.g., R¹, R^(a), etc.) occurs more than one time in any constituent or in formula I, its definition on each occurrence is independent of its definition at every other occurrence. Also, combinations of substituents and/or variables are permissible only if such combinations result in stable compounds. A squiggly line across a bond in a substituent variable represents the point of attachment.

Under standard nomenclature used throughout this disclosure, the terminal portion of the designated side chain is described last, preceded by the adjacent functionality toward the point of attachment.

In choosing compounds of the present invention, one of ordinary skill in the art will recognize that the various substituents, i.e. R¹, R², etc., are to be chosen in conformity with well-known principles of chemical structure connectivity and stability.

The term “substituted” means that one or more hydrogens on the designated atom is replaced with a selection from the indicated group, provided that the designated atom's normal valency under the existing circumstances is not exceeded, and that the substitution results in a stable compound. The term substituted shall be deemed to include multiple degrees of substitution by a named substitutent. Where multiple substituent moieties are disclosed or claimed, the substituted compound can be independently substituted by one or more of the disclosed or claimed substituent moieties, singly or plurally. By independently substituted, it is meant that the (two or more) substituents can be the same or different.

By “stable compound” or “stable structure” is meant a compound that is sufficiently robust to survive isolation to a useful degree of purity from a reaction mixture, and whose structure and properties remain or can be caused to remain essentially unchanged for a period of time sufficient to allow use of the compound for the purposes described herein (e.g., therapeutic administration to a subject). The compounds of the present invention are limited to stable compounds embraced by Formula I.

When a group, e.g., C₁-C₈ alkyl, is indicated as being substituted, such substitutions can also occur where such group is part of a larger substituent, e.g., —C₁-C₆alkyl-C₃-C₇cycloalkyl and —C₁-C₈alkyl-aryl.

In the compounds of Formula I, IA, and IB, the atoms may exhibit their natural isotopic abundances, or one or more of the atoms may be artificially enriched in a particular isotope having the same atomic number, but an atomic mass or mass number different from the atomic mass or mass number predominantly found in nature. The present invention is meant to include all suitable isotopic variations of the compounds of Formula I, IA, and IB. For example, different isotopic forms of hydrogen (H) include protium (H) and deuterium (²H or D). Protium is the predominant hydrogen isotope found in nature. Enriching for deuterium may afford certain therapeutic advantages, such as increasing in vivo half-life or reducing dosage requirements, or may provide a compound useful as a standard for characterization of biological samples. Isotopically-enriched compounds within Formula I, IA, and IB can be prepared without undue experimentation by conventional techniques well known to those skilled in the art or by processes analogous to those described in the EXAMPLES herein using appropriate isotopically-enriched reagents and/or intermediates.

Unless expressly stated to the contrary in a particular context, any of the various cyclic rings and ring systems described herein may be attached to the rest of the compound at any ring atom (i.e., any carbon atom or any heteroatom) provided that a stable compound results.

Unless expressly stated to the contrary, all ranges cited herein are inclusive. For example, a heteroaromatic ring described as containing from “1 to 4 heteroatoms” means the ring can contain 1, 2, 3 or 4 heteroatoms. It is also to be understood that any range cited herein includes within its scope all of the sub-ranges within that range. Thus, for example, a heterocyclic ring described as containing from “1 to 4 heteroatoms” is intended to include as aspects thereof, heterocyclic rings containing 2 to 4 heteroatoms, 3 or 4 heteroatoms, 1 to 3 heteroatoms, 2 or 3 heteroatoms, 1 or 2 heteroatoms, 1 heteroatom, 2 heteroatoms, 3 heteroatoms, and 4 heteroatoms. Similarly, C₁₋₆ when used with a chain, for example an alkyl chain, means that the chain can contain 1, 2, 3, 4, 5 or 6 carbon atoms. It also includes all ranges contained therein including C₁₋₅, C₁₋₄, C₁₋₃, C₁₋₂, C₂₋₆, C₃₋₆, C₄₋₆, C₅₋₆, and all other possible combinations.

It should also be noted that any carbon as well as heteroatom with unsatisfied valences in the text, schemes, examples and tables herein is assumed to have the sufficient number of hydrogen atom(s) to satisfy the valences.

When any substituent or variable (e.g., alkyl, R⁸, R¹¹, etc.) occurs more than one time in any constituent or in Formula (I), its definition on each occurrence is independent of its definition at every other occurrence, unless otherwise indicated.

The term “compound” refers to the free compound and, to the extent they are stable, any hydrate or solvate thereof. A hydrate is the compound complexed with water, and a solvate is the compound complexed with an organic solvent.

As indicated above, the compounds of the present invention can be employed in the form of pharmaceutically acceptable salts. It will be understood that, as used herein, the compounds of the instant invention can also include the pharmaceutically acceptable salts, and also salts that are not pharmaceutically acceptable when they are used as precursors to the free compounds or their pharmaceutically acceptable salts or in other synthetic manipulations.

The term “pharmaceutically acceptable salt” refers to a salt which possesses the effectiveness of the parent compound and which is not biologically or otherwise undesirable (e.g., is neither toxic nor otherwise deleterious to the recipient thereof). The term “pharmaceutically acceptable salt” refers to salts prepared from pharmaceutically acceptable non-toxic bases or acids including inorganic or organic bases and inorganic or organic acids. Salts of basic compounds encompassed within the term “pharmaceutically acceptable salt” refer to non-toxic salts of the compounds of this invention which are generally prepared by reacting the free base with a suitable organic or inorganic acid. Representative salts of basic compounds of the present invention include, but are not limited to, the following: acetate, ascorbate, adipate, alginate, aspirate, benzenesulfonate, benzoate, bicarbonate, bisulfate, bitartrate, borate, bromide, butyrate, camphorate, camphorsulfonate, camsylate, carbonate, chloride, clavulanate, citrate, cyclopentane propionate, diethylacetic, digluconate, dihydrochloride, dodecylsulfanate, edetate, edisylate, estolate, esylate, ethanesulfonate, formic, fumarate, gluceptate, glucoheptanoate, gluconate, glutamate, glycerophosphate, glycollylarsanilate, hemisulfate, heptanoate, hexanoate, hexylresorcinate, hydrabamine, hydrobromide, hydrochloride, 2-hydroxyethanesulfonate, hydroxynaphthoate, iodide, isonicotinic, isothionate, lactate, lactobionate, laurate, malate, maleate, mandelate, mesylate, methylbromide, methylnitrate, methylsulfate, methanesulfonate, mucate, 2-naphthalenesulfonate, napsylate, nicotinate, nitrate, N-methylglucamine ammonium salt, oleate, oxalate, pamoate (embonate), palmitate, pantothenate, pectinate, persulfate, phosphate/diphosphate, pimelic, phenylpropionic, polygalacturonate, propionate, salicylate, stearate, sulfate, subacetate, succinate, tannate, tartrate, teoclate, thiocyanate, tosylate, triethiodide, trifluoroacetate, undeconate, valerate and the like. Furthermore, where the compounds of the invention carry an acidic moiety, suitable pharmaceutically acceptable salts thereof include, but are not limited to, salts derived from inorganic bases including aluminum, ammonium, calcium, copper, ferric, ferrous, lithium, magnesium, manganic, mangamous, potassium, sodium, zinc, and the like. Particularly preferred are the ammonium, calcium, magnesium, potassium, and sodium salts. Salts derived from pharmaceutically acceptable organic non-toxic bases include salts of primary, secondary, and tertiary amines, cyclic amines, dicyclohexyl amines and basic ion-exchange resins, such as arginine, betaine, caffeine, choline, N,N-dibenzylethylenediamine, diethylamine, 2-diethylaminoethanol, 2-dimethylaminoethanol, ethanolamine, ethylamine, ethylenediamine, N-ethylmorpholine, N-ethylpiperidine, glucamine, glucosamine, histidine, hydrabamine, isopropylamine, lysine, methylglucamine, morpholine, piperazine, piperidine, polyamine resins, procaine, purines, theobromine, triethylamine, trimethylamine, tripropylamine, tromethamine, and the like. Also, included are the basic nitrogen-containing groups may be quaternized with such agents as lower alkyl halides, such as methyl, ethyl, propyl, and butyl chloride, bromides and iodides; dialkyl sulfates like dimethyl, diethyl, dibutyl; and diamyl sulfates, long chain halides such as decyl, lauryl, myristyl and stearyl chlorides, bromides and iodides, aralkyl halides like benzyl and phenethyl bromides and others.

These salts can be obtained by known methods, for example, by mixing a compound of the present invention with an equivalent amount and a solution containing a desired acid, base, or the like, and then collecting the desired salt by filtering the salt or distilling off the solvent. The compounds of the present invention and salts thereof may form solvates with a solvent such as water, ethanol, or glycerol. The compounds of the present invention may form an acid addition salt and a salt with a base at the same time according to the type of substituent of the side chain.

The compounds of the invention can also be employed in the form of a prodrug. For example, the hydrogen in —COOH be replaced with any the following groups: C₁₋₆ alkyl, C₃₋₆ cycloalkyl, —C₁₋₆alkyl-C₃₋₆cycloalkyl, C₃₋₇ cycloheteroalkyl, —C₁₋₆alkyl-C₃₋₇cycloheteroalkyl, aryl, —C₁₋₁₀alkyl-aryl, heteroaryl, and —C₁₋₁₀ alkyl-heteroaryl. Any C₁₋₆ alkyl, C₃₋₆ cycloalkyl, or C₃₋₇ cycloheteroalkyl can also be substituted. Any aryl or heteroaryl can also be substituted as indicated.

As set forth above, the present invention includes pharmaceutical compositions comprising a compound of Formula I, IA, or IB of the present invention, optionally one or more other active components, and a pharmaceutically acceptable carrier. The characteristics of the carrier will depend on the route of administration. By “pharmaceutically acceptable” is meant that the ingredients of the pharmaceutical composition must be compatible with each other, do not interfere with the effectiveness of the active ingredient(s), and are not deleterious (e.g., toxic) to the recipient thereof. Thus, compositions according to the invention may, in addition to the inhibitor, contain diluents, fillers, salts, buffers, stabilizers, solubilizers, and other materials well known in the art.

Also as set forth above, the present invention includes a method for treating a bacterial infection which comprises administering to a subject in need of such treatment a therapeutically effective amount of a compound of Formula I, IA, or IB or a pharmaceutically acceptable salt thereof. The term “subject” (or, alternatively, “patient”) as used herein refers to an animal, preferably a mammal, most preferably a human, who has been the object of treatment, observation or experiment. The term “administration” and variants thereof (e.g., “administering” a compound) in reference to a compound of Formula I, IA or IB mean providing the compound, or a pharmaceutically acceptable salt thereof, to the individual in need of treatment. When a compound or a salt thereof is provided in combination with one or more other active agents, “administration” and its variants are each understood to include provision of the compound or its salt and the other agents at the same time or at different times. When the agents of a combination are administered at the same time, they can be administered together in a single composition or they can be administered separately. It is understood that a “combination” of active agents can be a single composition containing all of the active agents or multiple compositions each containing one or more of the active agents. In the case of two active agents a combination can be either a single composition comprising both agents or two separate compositions each comprising one of the agents; in the case of three active agents a combination can be either a single composition comprising all three agents, three separate compositions each comprising one of the agents, or two compositions one of which comprises two of the agents and the other comprises the third agent; and so forth.

The compositions and combinations of the present invention are suitably administered in effective amounts. The term “effective amount” as used herein with respect to an oxazolidinone compound means the amount of active compound sufficient to cause a bacteriocidal or bacteriostatic effect. In one embodiment, the effective amount is a “therapeutically effective amount” meaning the amount of active compound that can overcome bacterial drug resistance and which is sufficient to inhibit bacterial replication and/or result in bacterial killing. When the active compound (i.e., active ingredient) is administered as the salt, references to the amount of active ingredient are to the free acid or free base form of the compound.

The administration of a composition of the present invention is suitably parenteral, oral, sublingual, transdermal, topical, intranasal, intratracheal, intraocular, or intrarectal, wherein the composition is suitably formulated for administration by the selected route using formulation methods well known in the art, including, for example, the methods for preparing and administering formulations described in chapters 39, 41, 42, 44 and 45 in Remington—The Science and Practice of Pharmacy, 21^(st) edition, 2006. In one embodiment, compounds of the invention are administered intravenously in a hospital setting. In another embodiment, administration is oral in the form of a tablet or capsule or the like. The dosage of the compounds of the invention and of their pharmaceutically acceptable salts may vary within wide limits and should naturally be adjusted, in each particular case, to the individual conditions and to the pathogenic agent to be controlled. In general, for a use in the treatment of bacterial infections, the daily dose may be between 0.005 mg/kg to 100 mg/kg, 0.01 mg/kg to 10 mg/kg, 0.05 mg/kg to 5 mg/kg, 0.05 mg/kg to 1 mg/kg.

In some embodiments, the compound of the invention is provided in a pharmaceutical formulation for oral, intravenous, intramuscular, nasal, or topical administration. Thus, in some embodiments, the formulation can be prepared in a dosage form, such as but not limited to, a tablet, capsule, liquid (solution or suspension), suppository, ointment, cream, or aerosol. In some embodiments, the presently disclosed subject matter provides such compounds and/or formulations that have been lyophilized and that can be reconstituted to form pharmaceutically acceptable formulations for administration, for example, as by intravenous or intramuscular injection.

Intravenous administration of a compound of the invention can be conducted by reconstituting a powdered form of the compound with an acceptable solvent. Suitable solvents include, for example, saline solutions (e.g., 0.9% Sodium Chloride Injection) and sterile water (e.g., Sterile Water for Injection, Bacteriostatic Water for Injection with methylparaben and propylparaben, or Bacteriostatic Water for Injection with 0.9% benzyl alcohol). The powdered form of the compound can be obtained by gamma-irradiation of the compound or by lyophilization of a solution of the compound, after which the powder can be stored (e.g., in a sealed vial) at or below room temperature until it is reconstituted. The concentration of the compound in the reconstituted IV solution can be, for example, in a range of from about 0.1 mg/mL to about 20 mg/mL.

The methods of the presently disclosed subject matter are useful for treating these conditions in that they inhibit the onset, growth, or spread of the condition, cause regression of the condition, cure the condition, or otherwise improve the general well-being of a subject afflicted with, or at risk of, contracting the condition. Thus, in accordance with the presently disclosed subject matter, the terms “treat”, “treating”, and grammatical variations thereof, as well as the phrase “method of treating”, are meant to encompass any desired therapeutic intervention, including but not limited to a method for treating an existing infection in a subject, and a method for the prophylaxis (i.e., preventing) of infection, such as in a subject that has been exposed to a microbe as disclosed herein or that has an expectation of being exposed to a microbe as disclosed herein.

Infections that may be treatable by the compounds of the invention can be caused by a variety of microbes, including fungi, algae, protozoa, bacteria, and viruses. In some embodiments, the infection is a bacterial infection. Exemplary microbial infections that may be treated by the methods of the invention include, but are not limited to, infections caused by one or more of Staphylococcus aureaus, Enterococcus faecalis, Bacillus anthracis, a Streptococcus species (e.g., Streptococcus pyogenes and Streptococcus pneumoniae), Escherichia coli, Pseudomonas aeruginosa, Burkholderia cepacia, a Proteus species (e.g., Proteus mirabilis and Proteus vulgaris), Klebsiella pneumoniae, Acinetobacter baumannii, Strenotrophomonas maltophillia, Mycobacterium tuberculosis, Mycobacterium bovis, other mycobacteria of the tuberculosis complex, and non-tuberculous mycobacteria, including Mycobacterium ulcerans.

In certain embodiments, the infection is an infection of a gram-positive bacterium. In some embodiments, the infection is selected from a mycobacterial infection, a Bacillus anthracis infection, an Enterococcus faecalis infection, and a Streptococcus pneumoniae infection.

In some embodiments, the compound of Formula I, IA, or IB is administered prophylactically to prevent or reduce the incidence of one of: (a) a Mycobacterium tuberculosis infection in a subject at risk of infection; (b) a recurrence of a Mycobacterium tuberculosis infection; and (c) combinations thereof. In some embodiments, the compound of Formula I, IA, or IB is administered to treat an existing Mycobacterium tuberculosis infection. In some embodiments, the compound of Formula I, IA, or IB is administered to treat an infection of a multi-drug resistant strain of Mycobacterium tuberculosis (i.e., a strain that is resistant to two or more previously known anti-tuberculosis drugs, such as isoniazid, ethambutol, rifampicin, kanamycin, capreomycin, linezolid, and streptomycin). In some embodiments, the compound of Formula (I) has a minimum inhibitory concentration (MIC) against Mycobacterium tuberculosis of 25 μg/mL or less. In some embodiments, the compound of Formula I, IA or IB is administered to treat an infection of a multi-drug resistant strain of Mycobacterium tuberculosis.

Thus, the methods of the presently disclosed subject matter can be useful for treating tuberculosis in that they inhibit the onset, growth, or spread of a TB infection, cause regression of the TB infection, cure the TB infection, or otherwise improve the general well-being of a subject afflicted with, or at risk of, contracting tuberculosis.

Subjects suffering from an M. tuberculosis or other tuberculosis-related infection can be determined via a number of techniques, e.g., sputum smear, chest X-ray, tuberculin skin test (i.e., Mantoux test or PPD test) and/or the presence of other clinical symptoms (e.g., chest pain, coughing blood, fever, night sweats, appetite loss, fatigue, etc.). If desired, bacterial RNA, DNA or proteins can be isolated from a subject believed to be suffering from TB and analyzed via methods known in the art and compared to known nucleic or amino acid sequences of bacterial RNA, DNA or protein.

In some embodiments, the compound of Formula I, IA, or IB has a minimum inhibitory concentration (MIC) against Mycobacterium tuberculosis of 25 μg/mL or less. MICs can be determined via methods known in the art, for example, as described in Hurdle et al., 2008, J. Antimicrob. Chemother. 62:1037-1045.

In some embodiments, the methods of the invention further comprise administering to the subject an additional therapeutic compound. In some embodiments, the compound of the invention is administered to the subject before, after, or at the same time as one or more additional therapeutic compounds. In some embodiments, the additional therapeutic compound is an antibiotic. In some embodiments, the additional therapeutic compound is an anti-tuberculosis therapeutic. In some embodiments, the additional therapeutic compound is selected from the group comprising isoniazid, ethambutol, rifampicin, kanamycin, capreomycin, linezolid, and streptomycin.

The invention thus provides in a further aspect, a combination comprising a compound of Formula I, IA, or IB or a pharmaceutically acceptable salt thereof, together with one or more additional therapeutic agents. Examples of such one or more additional therapeutic agents are anti-tuberculosis agents including, but not limited to, amikacin, aminosalicylic acid, capreomycin, cycloserine, ethambutol, ethionamide, isoniazid, kanamycin, pyrazinamide, rifamycins (such as rifampin, rifapentine and rifabutin), streptomycin, clarithromycin, azithromycin, oxazolidinones and fluoroquinolones (such as ofloxacin, ciprofloxacin, moxifloxacin and gatifloxacin). Such chemotherapy is determined by the judgment of the treating physician using preferred drug combinations. “First-line” chemotherapeutic agents used to treat a Mycobacterium tuberculosis infection that is not drug resistant include isoniazid, rifampin, ethambutol, streptomycin and pyrazinamide. “Second-line” chemotherapeutic agents used to treat a Mycobacterium tuberculosis infection that has demonstrated drug resistance to one or more “first-line” drugs include ofloxacin, ciprofloxacin, ethionamide, aminosalicylic acid, cycloserine, amikacin, kanamycin and capreomycin. In addition to the aforementioned, there are a number of new anti-tuberculosis therapeutic agents emerging from clinical studies that may also be employed as the one or more additional therapeutic agents in a combination with a compound of Formula I, IA, or IB including, but not limited to, TMC-207, OPC-67683, PA-824, LL-3858 and SQ-109.

Thus, the other antibiotic which may be combined with the compounds of formula I, IA, or IB, are for example rifampicin (=rifampin); isoniazid; pyrazinamide; amikacin; ethionamide; moxifloxacin; ethambutol; streptomycin; para-aminosalicylic acid; cycloserine; capreomycin; kanamycin; thioacetazone; quinolones/fluoroquinolones such as for example ofloxacin, ciprofloxacin, sparfloxacin; macrolides such as for example clarithromycin, clofazimine, amoxicillin with clavulanic acid; rifamycins; rifabutin; rifapentine.

In a further aspect, the one or more additional therapeutic agent is, for example, an agent useful for the treatment of tuberculosis in a mammal, therapeutic vaccines, antibacterial agents, anti-viral agents; antibiotics and/or agents for the treatment of HIV/AIDS. Examples of such therapeutic agents include isoniazid (INH), ethambutol, rifampin, pirazinamide, streptomycin, capreomycin, ciprofloxacin and clofazimine.

In one aspect, the one or more additional therapeutic agent is a therapeutic vaccine. A compound of Formula I, IA, or IB or a pharmaceutically acceptable salt thereof, may thus be administered in conjunction with vaccination against mycobacterial infection, in particular vaccination against Mycobacterium tuberculosis infection. Existing vaccines against mycobacterial infection include Bacillus Calmette Guerin (BCG). Vaccines currently under development for the treatment, prophylaxis or amelioration of mycobacterial infection include: modified BCG strains which recombinantly express additional antigens, cytokines and other agents intended to improve efficacy or safety; attenuated mycobacteria which express a portfolio of antigens more similar to Mycobacterium tuberculosis than BCG; and subunit vaccines. Subunit vaccines may be administered in the form of one or more individual protein antigens, or a fusion or fusions of multiple protein antigens, either of which may optionally be adjuvanted, or in the form of a polynucleotide encoding one or more individual protein antigens, or encoding a fusion or fusions of multiple protein antigens, such as where the polynucleotide is administered in an expression vector. Examples of subunit vaccines include, but are not limited to: M72, a fusion protein derived from the antigens Mtb32a and Mtb39; HyVac-1, a fusion protein derived from antigen 85b and ESAT-6; HyVac-4, a fusion protein derived from antigen 85b and Tb10.4; MVA85a, a modified vaccinia virus Ankara expressing antigen 85a; and Aeras-402, adenovirus 35 expressing a fusion protein derived from antigen 85a, antigen 85b and Tb10.4.

Abbreviations employed herein include the following:

ACN=acetonitrile; CBZ—Cl=benzyl chloroformate; CDCl₃=deuterated chloroform; DCM=dichloromethane; DIAD=diisopropyl diazodicarboxylate, DIEA=N,N-Diisopropylethylamine; DMF=N,N-dimethylformamide; DMSO=dimethyl sulfoxide; Et=ethyl; EtOAc=ethyl acetate; EtOH=ethanol; GFP=green fluorescent protein; HATU=(1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate), HET=heterocycle; H₂=hydrogen gas, HPLC=high-performance liquid chromatography; LC-MS=liquid chromatography/mass spectrometry; Me=methyl; MeOH=methanol; MIC=minimum inhibitory concentration; MW=molecular weight; MS=mass spectrometry; Mtb=Mycobacterium tuberculosis; Pd—C=palladium on carbon; RT=room temperature; TB=tuberculosis; TEA=triethylamine; TFA=trifluoroacetic acid; THF=tetrahydrofuran; and TBDMS=tert-butyl dimethylsilyl.

Methods for Making the Compounds of Formula (I):

The compounds of Formula (I) can be prepared according to the following reaction schemes and EXAMPLES, or modifications thereof, using readily available starting materials, reagents and conventional synthesis procedures. In these reactions, it is also possible to make use of variations which are themselves known to those of ordinary skill in this art, but are not mentioned in greater detail. Alternative synthetic pathways and analogous structures will be apparent to those skilled in the art of organic synthesis in light of the following reaction schemes and EXAMPLES.

Scheme A shows a method useful for making oxazolidinone compounds of formula A7, which correspond to the Compounds of Formula (I), wherein R¹ is CH₂NH₂ and A is as defined in the Summary of the Invention. The scheme below shows the synthesis of oxazolidinone analogs wherein A is introduced via a coupling reaction. The synthetic scheme has been discussed in detail in the literature (Org. Proc. Res. Dev. 2003, 533). The oxizolidinone A3 can be assembled in one step from the oxirane S1 and carbamate A2. Further modification of the hydroxy group via the azide intermediate A5 can provide the amine A6. At the final step, the Suzuki coupling reaction provides the desired compound A7, which can be used to synthesize compounds where R¹ is a derivative of CH₂NH₂.

Scheme B shows a method useful for making oxazolidinone compounds of formula B4, which correspond to the Compounds of Formula (I), wherein R¹ is a heterocycle such as imdazole, triazole or tetrazole, and A is as defined in the Summary of the Invention. In Scheme B, B1 is converted to B2 via the Suzuki coupling reaction, followed by the introduction of a hetereocycle via displacement of the mesylate intermediate B3 to afford B4.

Compounds of formula A7 and B4 may be further elaborated using methods that would be well-known to those skilled in the art of organic synthesis or, for example, the methods described in the Examples below, to make the full scope of the Compounds of Formula (I).

Example 1 Synthesis of (S)-5-(aminomethyl)-3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)oxazolidin-2-one

Step A: Synthesis of (R)-3-(4-bromo-3-fluorophenyl)-5-(hydroxymethyl)oxazolidin-2-one

To a solution of benzyl (4-bromo-3-fluorophenyl)carbamate (50.0 g, 154 mmol) in THF (600 mL) was added lithium tert-butoxide (37.0 g, 463 mmol) at 0° C. The mixture was stirred at 20° C. for 2 hours, and then (R)-oxiran-2-ylmethyl butyrate (44.5 g, 309 mmol) at 20° C. was added. The resulting mixture was stirred at 20° C. for 16 hours, and then concentrated HCl was added to adjust the pH to 7. The organic solvent was removed under reduced pressure, and the residue was diluted with EtOAc (400 mL), washed with water (400 mL×2) and brine (500 mL), dried over Na₂SO₄, filtered and concentrated to give the crude product, which was purified by column chromatography (SiO₂, PE:EtOAc=1:1) to give the product (R)-3-(4-bromo-3-fluorophenyl)-5-(hydroxymethyl)oxazolidin-2-one as a solid.

Step B: Synthesis of (R)-(3-(4-bromo-3-fluorophenyl)-2-oxooxazolidin-5-yl)methyl methanesulfonate

To a solution of (R)-3-(4-bromo-3-fluorophenyl)-5-(hydroxymethyl)oxazolidin-2-one (1.0 g, 3.45 mmol) in DCM (10 mL) was added N-ethyl-N-isopropylpropan-2-amine (1.2 mL, 6.89 mmol) and methanesulfonyl chloride (5.17 mmol) at 0° C. The reaction mixture was stirred at 28° C. for 2 hours, and then diluted with water (20 mL), extracted with DCM (20 mL×3). The organic layer was dried over Na₂SO₄, filtered and concentrated to give (R)-(3-(4-bromo-3-fluorophenyl)-2-oxooxazolidin-5-yl)methyl methanesulfonate as an oil. MS (ESI) m/z: 368.2, 370.2 [M+H⁺].

Step C: (R)-5-(azidomethyl)-3-(4-bromo-3-fluorophenyl)oxazolidin-2-one

To a solution of (R)-(3-(4-bromo-3-fluorophenyl)-2-oxooxazolidin-5-yl)methyl methanesulfonate (13.0 g, 31.8 mmol) in DMF (150 mL) was added sodium azide (2.5 g, 38.1 mmol) and the resulting mixture was stirred at 70° C. for 4 hours. Then, the mixture was diluted with EtOAc (200 mL), washed with water (200 mL×2) and brine (200 mL), dried over Na₂SO₄, filtered and concentrated to give the crude (R)-5-(azidomethyl)-3-(4-bromo-3-fluorophenyl)oxazolidin-2-one, which was taken to the next step without purification.

Step D: (S)-5-(aminomethyl)-3-(4-bromo-3-fluorophenyl)oxazolidin-2-one

To a solution of (R)-5-(azidomethyl)-3-(4-bromo-3-fluorophenyl)oxazolidin-2-one (13.0 g, 31.7 mmol) in THF (50 mL) was added water (5.72 mL, 317 mmol) and triphenylphosphine (20.81 g, 79 mmol), then the mixture was stirred at 70° C. for 12 hours. The reaction mixture was evaporated to remove the organic solvent, then water (20 mL) was added and the pH was adjusted to 4 using 1 M HCl. The resulting mixture was extracted with EtOAc (30 mL×3), then the pH of the aqueous layer was adjusted to 10 using Na₂CO₃ (3M). The aqueous layer was extracted with EtOAc (40 mL×4), the combined organic solvents were dried over Na₂SO₄, filtered and concentrated to dryness to give the crude (S)-5-(aminomethyl)-3-(4-bromo-3-fluorophenyl)oxazolidin-2-one as a solid, which was used in the next step without further purification. MS (ESI) m/z: 288.9, 290.9 [M+H⁺].

Step E: (S)-5-(aminomethyl)-3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)oxazolidin-2-one

To a solution of (S)-5-(aminomethyl)-3-(4-bromo-3-fluorophenyl)oxazolidin-2-one (3.0 g, 9.34 mmol), (4-(methylthio)phenyl)boronic acid (1.9 g, 11.21 mmol) and potassium phosphate tribasic (9.3 mL, 18.68 mmol) in THF (40 mL) was added 2^(nd) generation xphos precatalyst (0.7 g, 0.93 mmol) under N₂ atmosphere. The mixture was de-gassed and refilled with N₂ (3×). The mixture was stirred at 60° C. for 16 hours. Then, the mixture was concentrated to give the crude product, which was purified by column chromatography (SiO₂, PE:EtOAc=1:1 to DCM:MeOH=10:1) to give the desired product (S)-5-(aminomethyl)-3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)oxazolidin-2-one 1 as a solid. MS (ESI) m/z: 333.1 [M+H⁺] (calc'd 333.1).

The following compounds were made using the methods described in Example 1, substituting the appropriate reactants and/or reagents.

Mass Example Structure IUPAC Name M + H⁺ 2

4′-[(5S)-5-(aminomethyl)-2- oxo-1,3-oxazolidin-3-yl]-2′- fluorobiphenyl-4-carboxamide 330.1 3

(5S)-5-(aminomethyl)-3-[2- fluoro-3′- (methylsulfanyl)biphenyl-4-yl]- 1,3-oxazolidin-2-one 333.1 4

(5S)-5-(aminomethyl)-3-[2- fluoro-4′- (methylsulfonyl)biphenyl-4-yl]- 1,3-oxazolidin-2-one 365 5

(5S)-5-(aminomethyl)-3-(3- fluoro-4-[1,2,4]triazolo[1,5- a]pyridin-6-ylphenyl)-1,3- oxazolidin-2-one 328.1 6

4′-[(5S)-5-(aminomethyl)-2- oxo-1,3-oxazolidin-3-yl]-2′- fluorobiphenyl-4-sulfonamide 366 7

(5S)-5-(aminomethyl)-3-[2- fluoro-4′- (methylsulfinyl)biphenyl-4-yl]- 1,3-oxazolidin-2-one 349.1 8

(5S)-5-(aminomethyl)-3-(3- fluoro-4-[1,2,4]triazolo[1,5- a]pyridin-7-ylphenyl)-1,3- oxazolidin-2-one 328.1 9

(5S)-5-(aminomethyl)-3-(3- fluoro-4-[1,2,4]triazolo[4,3- a]pyridin-6-ylphenyl)-1,3- oxazolidin-2-one 328.1 10

4′-[(5S)-5-(aminomethyl)-2- oxo-1,3-oxazolidin-3-yl]-2′- fluorobiphenyl-3-carboxamide 330 11

(5S)-5-(aminomethyl)-3-(2- fluoro-4′-hydroxybiphenyl-4- yl)-1,3-oxazolidin-2-one 303.1 12

(5S)-5-(aminomethyl)-3-(3- fluoro-4-furan-3-ylphenyl)-1,3- oxazolidin-2-one 277.1 13

4′-[(5S)-5-(aminomethyl)-2- oxo-1,3-oxazolidin-3-yl]-2′- fluorobiphenyl-3-carbonitrile 312.1 14

4′-[(5S)-5-(aminomethyl)-2- oxo-1,3-oxazolidin-3-yl]-2′- fluoro-N,N-dimethylbiphenyl-4- sulfonamide 394 15

(5S)-5-(aminomethyl)-3-(3- fluoro-4-thiophen-3-ylphenyl)- 1,3-oxazolidin-2-one 292.8 16

(5S)-5-(aminomethyl)-3-[3- fluoro-4-(1H-pyrazol-5- yl)phenyl]-1,3-oxazolidin-2-one 277 17

N-{4′-[(5S)-5-(aminomethyl)-2- oxo-1,3-oxazolidin-3-yl]-2′- fluorobiphenyl-4- yl}methanesulfonamide 380 18

4′-[(5S)-5-(aminomethyl)-2- oxo-1,3-oxazolidin-3-yl]-2′- fluorobiphenyl-4-carbonitrile 312 19

(5S)-5-(aminomethyl)-3-[3- fluoro-4-(6-fluoropyridin-3- yl)phenyl]-1,3-oxazolidin-2-one 306.1 20

(5S)-5-(aminomethyl)-3-(2- fluoro-3′-nitrobiphenyl-4-yl)- 1,3-oxazolidin-2-one 332 21

(5S)-5-(aminomethyl)-3-[3′- (1,1-dioxidothiomorpholin-4- yl)-2-fluorobiphenyl-4-yl]-1,3- oxazolidin-2-one 420 22

(5S)-5-(aminomethyl)-3-[4-(6- chloropyridin-3-yl)-3- fluorophenyl]-1,3-oxazolidin-2- one 322 23

(5S)-5-(aminomethyl)-3-{3- fluoro-4-[2-(1-hydroxy-1- methylethyl)-1,3-thiazol-5- yl]phenyl}-1,3-oxazolidin-2- one 352 24

(5S)-5-(aminomethyl)-3-(3- fluoro-4-pyridin-3-ylphenyl)- 1,3-oxazolidin-2-one 288 25

(5S)-5-(aminomethyl)-3-(3- fluoro-4-pyrimidin-5-ylphenyl)- 1,3-oxazolidin-2-one 289 26

tert-butyl 4-{4-[(5S)-5- (aminomethyl)-2-oxo-1,3- oxazolidin-3-yl]-2- fluorophenyl}-3,6- dihydropyridine-1(2H)- carboxylate 27

(5S)-5-(aminomethyl)-3-[3- fluoro-4-(1H-indol-6- yl)phenyl]-1,3-oxazolidin-2-one 326.1 28

(5S)-5-(aminomethyl)-3-[3- fluoro-4-(2-methoxypyrimidin- 5-yl)phenyl]-1,3-oxazolidin-2- one 319.1 29

(5S)-5-(aminomethyl)-3-{3- fluoro-4-[2-(1,4-oxazepan-4- yl)pyrimidin-5-yl]phenyl}-1,3- oxazolidin-2-one 388.1 30

(5S)-5-(aminomethyl)-3-[4-(2- chloropyridin-4-yl)-3- fluorophenyl]-1,3-oxazolidin-2- one 322.2 31

(5S)-5-(aminomethyl)-3-[3- fluoro-4-(1H-pyrrolo[2,3- b]pyridin-4-yl)phenyl]-1,3- oxazolidin-2-one 327.1 32

(5S)-5-(aminomethyl)-3-{3- fluoro-4-[2- (methylsulfanyl)pyrimidin-5- yl]phenyl}-1,3-oxazolidin-2- one 335.1 33

(5S)-5-(aminomethyl)-3-[4-(6- cyclopropylpyridin-3-yl)-3- fluorophenyl]-1,3-oxazolidin-2- one 328.1 34

5-{4-[(5S)-5-(aminomethyl)-2- oxo-1,3-oxazolidin-3-yl]-2- fluorophenyl}-2,3-dihydro-1H- isoindol-1-one 342.1 35

(5S)-5-(aminomethyl)-3-[3- fluoro-4-(1H-pyrrolo[2,3- c]pyridin-4-yl)phenyl]-1,3- oxazolidin-2-one 327.1 36

(5S)-5-(aminomethyl)-3-{4-[1- (difluoromethyl)-1H-pyrazol-4- yl]-3-fluorophenyl}-1,3- oxazolidin-2-one 327.1 37

(5S)-5-(aminomethyl)-3-[3- fluoro-4-(1-methyl-1H-pyrazol- 4-yl)phenyl]-1,3-oxazolidin-2- one 291.1 38

(5S)-5-(aminomethyl)-3-(3- fluoro-4-pyrazolo[1,5- b]pyridazin-3-ylphenyl)-1,3- oxazolidin-2-one 328 39

(5S)-5-(aminomethyl)-3-(2- fluorobiphenyl-4-yl)-1,3- oxazolidin-2-one 287

Example 40 Synthesis of (S)—N-((3-(5-fluoro-6-(4-(methylthio)phenyl)pyridin-3-yl)-2-oxooxazolidin-5-yl)methyl)acetamide

Step A: Synthesis of (S,E)-1-(benzylideneamino)-3-chloropropan-2-ol

To a solution of (S)-2-(chloromethyl)oxirane (5.0 g, 54.3 mmol) in EtOH (15 mL) was added ammonia hydrate (4.9 g, 140 mmol) and benzaldehyde (5.98 g, 56.4 mmol) and the resulting mixture was stirred at 40° C. for 16 hours. The reaction mixture was concentrated to give (S,E)-1-(benzylideneamino)-3-chloropropan-2-ol as a solid, which was used in the next step without purification.

Step B: Synthesis of (S)-1-amino-3-chloropropan-2-ol hydrochloride

To a solution of (S,E)-1-(benzylideneamino)-3-chloropropan-2-ol (6.2 g, 31.4 mmol) in EtOH (13 mL) and Toluene (12 mL) was added HCl (6.8 mL, 83 mmol) and the resulting mixture was stirred at 35° C. for 4 hours. The reaction mixture was concentrated to smaller volume, washed with water (20 mL), and the aqueous extract was lyophilized to give (S)-1-amino-3-chloropropan-2-ol hydrochloride as a solid. The crude product was taken to the next step without further purification.

Step C: Synthesis of (S)-1-acetamido-3-chloropropan-2-yl acetate

To a solution of (S)-1-amino-3-chloropropan-2-ol hydrochloride (28.0 g, 153 mmol) in DCM (100 mL) was added acetic anhydride (36.0 g, 353 mmol), pyridine (15.3 g, 193 mmol) and the resulting mixture was stirred at 35° C. for 16 hours. Then K₂CO₃ (42.0 g, 304 mmol) was added portion-wise, maintaining the temperature at 5-7° C., then 0.5N HCl (250 mL) was added, and the resulting mixture was diluted with H₂O (250 mL), and extracted with DCM (200 mL×3). The organic layer was dried over Na₂SO₄, filtered and concentrated to give (S)-1-acetamido-3-chloropropan-2-yl acetate as a solid. The crude product was used directly in the next step without further purification. MS (ESI) m/z: 217.3 [M+Na⁺].

Step D: Synthesis of (S)—N-((3-(6-chloro-5-fluoropyridin-3-yl)-2-oxooxazolidin-5-yl)methyl)acetamide

To a solution of benzyl (6-chloro-5-fluoropyridin-3-yl)carbamate (6 g, 21.38 mmol) in DMF (20 mL) was added MeOH (1.730 mL, 42.8 mmol), and then a solution of lithium tert-butoxide (5.1 g, 64.1 mmol) in THF (30 mL) was added drop-wise at 0° C. The resulting mixture was slowly warmed to 16° C. and stirred for 2 hours. Then (S)-1-acetamido-3-chloropropan-2-yl acetate (8.3 g, 42.8 mmol) was added to this reaction mixture and stirred at 16° C. for 12 hours. The mixture was concentrated to remove the THF, and diluted with EtOAc (20 mL), the organic layer was washed with H₂O (25 mL×3), dried over Na₂SO₄, filtered and concentrated to dryness to give the crude product, which was purified by column chromatography on silica gel (0 to 90% DCM/MeOH) to give (S)—N-((3-(6-chloro-5-fluoropyridin-3-yl)-2-oxooxazolidin-5-yl)methyl)acetamide as a solid. MS (ESI) m/z: 287.8[M+H⁺].

Step E: Synthesis of (S)—N-((3-(5-fluoro-6-(4-(methylthio)phenyl)pyridin-3-yl)-2-oxooxazolidin-5-yl)methyl)acetamide 40

To a solution of (S)—N-((3-(6-chloro-5-fluoropyridin-3-yl)-2-oxooxazolidin-5-yl)methyl)acetamide (80.0 mg, 0.278 mmol), (4-(methylthio)phenyl)boronic acid (46.7 mg, 0.278 mmol) and potassium phosphate tribasic (118.0 mg, 0.556 mmol) in THF (2 mL) was added 2nd generation xphos precatalyst (21.9 mg, 0.028 mmol) under N₂ atmosphere. The mixture was de-gassed and refilled with N₂ (3×). The mixture was stirred at 60° C. for 16 hours. The reaction mixture was concentrated to give the crude product, which was purified by reverse phase prep-HPLC to give (S)—N-((3-(5-fluoro-6-(4-(methylthio)phenyl)pyridin-3-yl)-2-oxooxazolidin-5-yl)methyl)acetamide 40 as a solid. LC/MS=376.1 [M+H⁺].

Example 41 Synthesis of (S)—N-((3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl)cyclopropanecarboxamide

To a solution of cyclopropanecarboxylic acid (14.2 mg, 0.165 mmol) in DMF (2 mL) was added DIEA (53 mL, 0.301 mmol) and HATU (62.9 mg, 0.165 mmol). The mixture was stirred at 20° C. for 15 minutes and then (S)-5-(aminomethyl)-3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)oxazolidin-2-one (50.0 mg, 0.150 mmol) was added. The mixture was stirred at 20° C. for 16 hours. The reaction mixture was filtered, and concentrated to give a residue which was purified by reverse phase prep-HPLC to give (S)—N-((3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl)cyclopropanecarboxamide as a solid. LC/MS=401.1 [M+H⁺].

Example 42 Synthesis of (S)—N-((3-(4-(5,6-dihydro-[1,2,4]triazolo[1,5-a]pyrazin-7(8H)-yl)phenyl)-2-oxooxazolidin-5-yl)methyl)acetamide

Step A: Synthesis of benzyl (4-bromophenyl)carbamate

To a solution of 4-bromoaniline (50.0 g, 291 mmol) in acetone (500 mL) at 0° C. was added benzyl carbonochloridate (54.5 g, 320 mmol) to form a white slurry. Then a solution of sodium bicarbonate (581 mL, 581 mmol) was added slowly. After addition, the mixture was allowed to warm to room temperature and stirred for 16 hours. Organic solvent was removed under reduced pressure, and the precipitated solid was collected by filtration and washed with water (200 mL×2). The solid was then dried to afford benzyl (4-bromophenyl)carbamate as a solid.

Step B: Synthesis of (S)—N-((3-(4-bromophenyl)-2-oxooxazolidin-5-yl)methyl)acetamide

To a solution of benzyl (4-bromophenyl)carbamate (10.0 g, 32.7 mmol) in the mixture of DMF (40 mL) and MeOH (2.6 mL, 65.3 mmol) was added a solution of lithium 2-methylpropan-2-olate (7.8 g, 98.0 mmol) in THF (60 mL) at 0° C., and then (S)-1-acetamido-3-chloropropan-2-yl acetate (12.6 g, 65.3 mmol) was added. The mixture was warmed to 20° C. and stirred for 16 hours. The mixture was concentrated to give a residue which was poured into ice-water (100 mL) and the solid was precipitated. The mixture was filtered, and the solid was washed with 100 mL of PE and dried in vacuum to give (S)—N-((3-(4-bromophenyl)-2-oxooxazolidin-5-yl)methyl)acetamide as a solid. MS (ESI) m/z: 313.0 [M+H⁺]. ¹H NMR (400 MHz, DMSO-d6) δ 8.30-8.22 (m, 1H), 7.60-7.54 (m, 2H), 7.54-7.48 (m, 2H), 4.72 (dd, J=6.0, 8.2 Hz, 1H), 4.10 (t, J=8.9 Hz, 1H), 3.73 (dd, J=6.6, 8.8 Hz, 1H), 3.41 (t, J=5.4 Hz, 2H), 1.83 (s, 3H). MS (ESI) m/z: 313.0, 315.0 [M+H⁺].

Step C: Synthesis of (S)—N-((3-(4-(5,6-dihydro-[1,2,4]triazolo[1,5-a]pyrazin-7(8H)-yl)phenyl)-2-oxooxazolidin-5-yl)methyl)acetamide

To a solution of (S)—N-((3-(4-bromophenyl)-2-oxooxazolidin-5-yl)methyl)acetamide (100.0 mg, 0.319 mmol), 5,6,7,8-tetrahydro-[1,2,4]triazolo[1,5-a]pyrazine (150.0 mg, 1.208 mmol) and Cs₂CO₃ (312.0 mg, 0.958 mmol) in 1,4-Dioxane (2 mL) was added 2nd generation ruphos precatalyst (12.4 mg, 0.016 mmol) under N₂ atmosphere. The mixture was stirred at 100° C. for 16 hours. The reaction mixture was concentrated to give a residue which was purified by reverse phase prep-HPLC to give (S)—N-((3-(4-(5,6-dihydro-[1,2,4]triazolo[1,5-a]pyrazin-7(8H)-yl)phenyl)-2-oxooxazolidin-5-yl)methyl)acetamide as solid. MS(ESI) m/z: 357.1 [M+H⁺].

Example 43 Synthesis of (R)-5-((1H-1,2,4-triazol-1-yl)methyl)-3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)oxazolidin-2-one

Step A: Synthesis of (R)-3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-5-(hydroxymethyl)oxazolidin-2-one

To a solution of (R)-3-(4-bromo-3-fluorophenyl)-5-(hydroxymethyl)oxazolidin-2-one (5.0 g, 17.24 mmol) and (4-(methylthio)phenyl)boronic acid (3.5 g, 20.68 mmol) in THF (60 mL) was added aqueous potassium phosphate (17.2 mL, 34.5 mmol) followed by 2nd generation xphos precatalyst (0.7 g, 0.862 mmol) under N₂ atmosphere. The resulting mixture was stirred at 60° C. for 16 hours. Then, the mixture was filtered and concentrated to give a residue which was purified by chromatography on silica gel (20% to 100% EtOAc in PE) to give (R)-3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-5-(hydroxymethyl)oxazolidin-2-one as a solid. ¹H NMR (400 MHz, DMSO-d6) δ 7.66-7.32 (m, 7H), 5.25-5.22 (m, 1H), 4.74-4.70 (m, 1H), 4.13-4.08 (m, 1H), 3.87-3.83 (m, 1H), 3.70-3.65 (m, 1H), 3.58-3.54 (m, 1H), 2.47 (s, 3H).

Step B: (R)-(3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl methanesulfonate

To a solution of (R)-3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-5-(hydroxymethyl)oxazolidin-2-one (500.0 mg, 1.50 mmol) in DCM (10 mL) was added DIEA (0.5 mL, 3.00 mmol) and MsCl (0.2 mL, 2.25 mmol) at 0° C. The resulting mixture was stirred at 20° C. for 2 hours. The reaction mixture was quenched with water (5 mL), and then was diluted with DCM (20 mL), washed with water (20 mL×2) and followed by with brine (20 mL), dried over Na₂SO₄, filtered and concentrated to give the crude product (R)-(3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl methanesulfonate as a solid. Crude material was used in the next step of the synthesis without further purification.

Step C: Synthesis of (R)-5-((1H-1,2,4-triazol-1-yl)methyl)-3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)oxazolidin-2-one

To a solution of 4H-1,2,4-triazole (12.6 mg, 0.18 mmol) in DMF (4 mL) were added K₂CO₃ (50.4 mg, 0.36 mmol) and (R)-(3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl methanesulfonate (50.0 mg, 0.12 mmol). The resulting mixture was stirred at 20° C. for 24 hours. The reaction mixture was quenched with saturated NH₄Cl (5 mL), and then was diluted with EtOAc (20 mL), washed with water (20 mL×2) and brine (20 mL), dried over Na₂SO₄, filtered and concentrated to give a residue which was purified by reverse phase prep-HPLC to provide (R)-5-((1H-1,2,4-triazol-1-yl)methyl)-3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)oxazolidin-2-one as a solid. LC/MS, m/z: 385.0 [M+H⁺].

The following compounds were made using the methods described in Example 43, substituting the appropriate reactants and/or reagents.

Example Structure IUPAC Name (M + H) 44

(5R)-3-[2-fluoro-4′- (methylsulfanyl)biphenyl-4- yl]-5-(1H-tetrazol-1-ylmethyl)- 1,3-oxazolidin-2-one 386.1 45

(5R)-3-[2-fluoro-4′- (methylsulfanyl)biphenyl-4- yl]-5-(1H-imidazol-1- ylmethyl)-1,3-oxazolidin-2-one 384.1 46

(5R)-3-[2-fluoro-4′- (methylsulfanyl)biphenyl-4- yl]-5-(1H-pyrazol-1-ylmethyl)- 1,3-oxazolidin-2-one 384.1

Example 47 Synthesis of (S)—N-((3-(2,6-difluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl)acetamide

Step A: Synthesis of benzyl (4-bromo-3,5-difluorophenyl)carbamate

To the stirring solution of 4-bromo-3,5-difluoroaniline (20 g, 96 mmol) in acetone (200 mL) at 0° C. was added benzyl carbonochloridate (18.04 g, 106 mmol) to form white slurry. Then sodium bicarbonate (192 mL, 192 mmol) was added in portions. After the addition, the mixture was allowed to warm to 25° C. and stirred for 16 hours. The organic solvent was removed under reduced pressure and the precipitated solid was collected by filtration, and washed with water (50 mL×2). The solid was then dried to afford benzyl (4-bromo-3,5-difluorophenyl)carbamate as a solid. ¹HNMR (CDCl₃, 400 MHz) δ 7.39-7.37 (m, 5H), 7.11-7.09 (dd, J=2.0, 6 Hz, 2H), 5.20 (s, 2H).

Step B: (S)—N-((3-(4-bromo-3,5-difluorophenyl)-2-oxooxazolidin-5-yl)methyl)acetamide

To a solution of benzyl (4-bromo-3,5-difluorophenyl)carbamate (8 g, 23.38 mmol)) in a mixture DMF (24 mL) and methanol (1.513 g, 47.2 mmol) was added a solution of lithium 2-methylpropan-2-olate (5.62 g, 70.1 mmol) in THF (48 mL). The resulting mixture was cooled to 5° C., then (S)-1-acetamido-3-chloropropan-2-yl acetate (9.06 g, 46.8 mmol) was added. The reaction mixture was stirred at 20° C. for 16 hours, and then was quenched by the addition of saturated NH₄Cl (50.0 mL). The precipitated solid was collected, washed with water (50 mL) and dried to provide (S)—N-((3-(4-bromo-3,5-difluorophenyl)-2-oxooxazolidin-5-yl)methyl)acetamide as a solid. MS (ESI) m/z: 348.8, 350.8 [M+H⁺].

Step C: (S)—N-((3-(2,6-difluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl)acetamide 47

To a solution of (S)—N-((3-(4-bromo-3,5-difluorophenyl)-2-oxooxazolidin-5-yl)methyl)acetamide (40.0 mg, 0.12 mmol), (4-(methylthio)phenyl)boronic acid (28.9 mg, 0.17 mmol), aqueous potassium phosphate (0.23 mL, 0.23 mmol) in THF (1 mL) was added 2nd generation xphos precatalyst (4.5 mg, 5.73 μmol) under N₂ atmosphere. The mixture was stirred at 60° C. for 16 hours. The reaction mixture was filtered and concentrated to give a residue which was purified by reverse phase prep-HPLC to provide (S)—N-((3-(2,6-difluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl)acetamide as a solid. LC/MS, m/z: 393.1 [M+H⁺].

Example 48 Synthesis of (S)-5-(aminomethyl)-3-(6-(1,1-dioxidothiomorpholino)-5-fluoropyridin-3-yl)oxazolidin-2-one

Step A: Synthesis of 4-(3-fluoro-5-nitropyridin-2-yl)thiomorpholine

To a solution of 2-chloro-3-fluoro-5-nitropyridine (3.0 g, 15.3 mmol) in DMF (30 mL) was added thiomorpholine (1.6 g, 15.3 mmol) and DIEA (5.3 mL, 30.6 mmol). The mixture was stirred at 60° C. for 16 hours. The reaction was cooled to room temperature, and then then was diluted with water (50 mL). The precipitated solid was collected by filtration, and dried to give 4-(3-fluoro-5-nitropyridin-2-yl)thiomorpholine as a solid. ¹HNMR δ 8.87 (s, 1H), 7.98 (dd, J=2.0, 13.6 Hz, 1H), 4.15-4.12 (m, 4H), 2.76-2.74 (m, 4H).

Step B: Synthesis of 5-fluoro-6-thiomorpholinopyridin-3-amine

To a solution of 4-(3-fluoro-5-nitropyridin-2-yl)thiomorpholine (4.0 g, 14.8 mmol) in Water (20 mL) and HOAc (20 mL) was added iron (4.1 g, 74.0 mmol). The resulting mixture was stirred at 60° C. for 4 hours. The reaction mixture was concentrated and then was diluted with EtOAc (100 mL), washed with saturated NaHCO₃ (80 mL×2) and then with brine (80 mL). The organic layer was dried over Na₂SO₄, filtered and concentrated to give 5-fluoro-6-thiomorpholinopyridin-3-amine as a solid. The crude material was used in the next step without further purification.

Step C: Synthesis of benzyl (5-fluoro-6-thiomorpholinopyridin-3-yl)carbamate

To the stirring solution of 5-fluoro-6-thiomorpholinopyridin-3-amine (3.1 g, 13.1 mmol) in acetone (30 mL) at 0° C. was added CBZ—Cl (2.2 mL, 15.7 mmol) to form a slurry. Then a solution of sodium bicarbonate (26.2 mL, 26.2 mmol) was added slowly. After the addition, the mixture was allowed to warm to 20° C. and was stirred for 16 hours. Organic solvent was removed under reduced pressure and the precipitated solid was collected by filtration, washed with water (40 mL×2) and dried to afford benzyl (5-fluoro-6-thiomorpholinopyridin-3-yl)carbamate as a solid. ¹HNMR (CDCl₃, 400 MHz) δ 7.83 (s, 1H), 7.75-7.72 (m, 1H), 7.39-7.35 (m, 5H), 6.61 (s, 1H), 5.20 (s, 2H), 3.71-3.68 (m, 4H), 2.75-2.67 (m, 4H).

Step D: Synthesis of (S)—N-((3-(5-fluoro-6-thiomorpholinopyridin-3-yl)-2-oxooxazolidin-5-yl)methyl)acetamide

To a solution of benzyl (5-fluoro-6-thiomorpholinopyridin-3-yl)carbamate (4.1 g, 10.6 mmol) in a mixture of DMF (15 mL) and MeOH (0.9 mL, 21.2 mmol) was added a solution of lithium tert-butoxide (2.6 g, 31.9 mmol) in THF (30 mL) at 0° C. The resulting mixture was stirred at 20° C. for 0.5 hours, and then (S)-1-acetamido-3-chloropropan-2-yl acetate (4.1 g, 21.2 mmol) was added at 20° C. The reaction mixture was stirred at 20° C. for 16 hours. The mixture was quenched with concentrated HCl (10 mL) and then concentrated to give the crude product, which was purified by column chromatography (SiO₂, PE:EtOAc=1:1 to DCM:MeOH=10:1) to give (S)—N-((3-(5-fluoro-6-thiomorpholinopyridin-3-yl)-2-oxooxazolidin-5-yl)methyl)acetamide as a solid. ¹HNMR (CDCl₃, 400 MHz) δ 8.06 (d, J=2 Hz, 1H), 7.90 (dd, J=2.4, 14.8 Hz, 1H), 4.84-4.78 (m, 1H), 4.14-4.12 (m, 1H), 3.81-3.70 (m, 5H), 3.57-3.56 (m, 2H), 2.74-2.71 (m, 4H), 1.97 (s, 3H).

Step E: Synthesis of (S)—N-((3-(6-(1,1-dioxidothiomorpholino)-5-fluoropyridin-3-yl)-2-oxooxazolidin-5-yl)methyl)acetamide

To a solution of (S)—N-((3-(5-fluoro-6-thiomorpholinopyridin-3-yl)-2-oxooxazolidin-5-yl)methyl)acetamide (300 mg, 0.76 mmol) in MeOH (3 mL) and water (1.5 mL) was added oxone (703 mg, 1.14 mmol) at 0° C. The mixture was stirred at 20° C. for 2 hours. The reaction mixture was concentrated to give the crude product, which was purified by prep-HPLC to give (S)—N-((3-(6-(1,1-dioxidothiomorpholino)-5-fluoropyridin-3-yl)-2-oxooxazolidin-5-yl)methyl)acetamide as a solid. ¹HNMR (DMSO-d6, 400 MHz) δ 8.25-8.22 (m, 1H), 8.13 (s, 1H), 7.93 (dd, J=1.6, 14.8 Hz, 1H), 4.77-4.72 (m, 1H), 4.11-4.07 (m, 1H), 3.84 (s, 4H), 3.73-3.69 (m, 1H), 3.41-3.39 (m, 2H), 3.20 (s, 4H), 1.82 (s, 3H). MS (ESI) m/z: 387.0 [M+H⁺].

Step F: (S)-5-(aminomethyl)-3-(6-(1,1-dioxidothiomorpholino)-5-fluoropyridin-3-yl)oxazolidin-2-one 48

To a solution of (S)—N-((3-(6-(1,1-dioxidothiomorpholino)-5-fluoropyridin-3-yl)-2-oxooxazolidin-5-yl)methyl)acetamide (150 mg, 0.39 mmol) in MeOH (2 mL) and water (0.5 mL) was added HCl (0.5 mL, 6.09 mmol). The mixture was stirred at 70° C. for 16 hours. The mixture was concentrated to give the crude product, which was purified by reverse phase prep-HPLC to give (S)-5-(aminomethyl)-3-(6-(1,1-dioxidothiomorpholino)-5-fluoropyridin-3-yl)oxazolidin-2-one 48 as a solid. ¹HNMR (CDCl₃, 400 MHz) δ 8.21 (s, 3H), 8.11 (s, 1H), 7.92 (dd, J=2.0, 14.8 Hz, 1H), 4.95-4.88 (m, 1H), 4.18-4.14 (m, 1H), 3.84-3.77 (m, 5H), 3.23-3.19 (m, 6H). MS (ESI) m/z: 345.0 [M+H⁺].

Examples 49 and 50 Synthesis of (R)-3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-5-((isoxazol-3-yloxy)methyl)oxazolidin-2-one

Step A: (R)-3-(4-bromo-3-fluorophenyl)-5-((isoxazol-3-yloxy)methyl)oxazolidin-2-one and (R)-2-((3-(4-bromo-3-fluorophenyl)-2-oxooxazolidin-5-yl)methyl)isoxazol-3(2H)-one

To a solution of triphenylphosphine (2.2 g, 8.3 mmol) in dry THF (50 mL) was added DIAD (1.6 mL, 8.3 mmol), and the resulting mixture was stirred for 0.5 hours. To this reaction mixture was added isoxazol-3-ol (645 mg, 7.6 mmol) and the mixture was stirred for 0.5 hours and then (R)-3-(4-bromo-3-fluorophenyl)-5-(hydroxymethyl)oxazolidin-2-one (2.0 g, 6.9 mmol) was added. The resulting mixture was stirred at 20° C. for 16 hours. The reaction mixture was diluted with EtOAc (200 mL), washed with hydrochloric acid (1M, 50 mL), then with water (50 mL) and brine (50 mL), dried over Na₂SO₄, and filtered. The filtrate was evaporated under reduced pressure. The residue was purified by column chromatography (SiO₂, PE to EtOAc) to give (R)-3-(4-bromo-3-fluorophenyl)-5-((isoxazol-3-yloxy)methyl)oxazolidin-2-one as solid (major product) and (R)-2-((3-(4-bromo-3-fluorophenyl)-2-oxooxazolidin-5-yl)methyl)isoxazol-3(2H)-one as a solid (minor product).

(R)-3-(4-bromo-3-fluorophenyl)-5-((isoxazol-3-yloxy)methyl)oxazolidin-2-one ¹H NMR (CDCl₃, 400 MHz) δ 8.16 (d, J=1.6 Hz, 1H), 7.66 (dd, J=7.2, 11.6 Hz, 1H), 7.39-7.58 (m, 4H), 7.17 (dd, J=1.6, 8.8 Hz, 1H), 6.00 (d, J=1.6 Hz, 1H), 4.89-5.11 (m, 2H), 4.43-4.63 (m, 2H), 4.15 (t, J=8.8 Hz, 1H), 3.96 (dd, J=6.4, 8.8 Hz, 1H).

(R)-2-((3-(4-bromo-3-fluorophenyl)-2-oxooxazolidin-5-yl)methyl)isoxazol-3(2H)-one ¹H NMR (CDCl₃, 400 MHz) δ 7.88 (d, J=2.4 Hz, 1H), 7.40-7.59 (m, 3H), 7.04-7.17 (m, 1H), 5.82 (d, J=2.4 Hz, 1H), 4.91-5.02 (m, 1H), 4.17-4.38 (m, 2H), 4.11 (t, J=8.8 Hz, 1H), 3.96 (dd, J=5.6, 9.2 Hz, 1H).

Step B: (R)-3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-5-((isoxazol-3-yloxy)methyl)oxazolidin-2-one

The 2nd generation xphos precatalyst (66.1 mg, 0.08 mmol) was added to the mixture of (R)-3-(4-bromo-3-fluorophenyl)-5-((isoxazol-3-yloxy)methyl)oxazolidin-2-one (300.0 mg, 0.84 mmol), (4-(methylthio)phenyl)boronic acid (155 mg, 0.924 mmol), potassium phosphate tribasic (357.0 mg, 1.68 mmol) in THF (5 mL) and water (1.5 mL) under N₂ protection. The mixture was stirred at 70° C. for 16 hours. LCMS showed most starting material was consumed and 50% of the desired product was formed. The mixture was cooled, water (10 mL) was added and the mixture was extracted with ethyl acetate (20 mL×2). The combined organic fractions were washed with brine (20 mL), dried over Na₂SO₄, filtered and concentrated. The residue was purified by reverse-phase Prep-HPLC to give (R)-3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-5-((isoxazol-3-yloxy)methyl)oxazolidin-2-one, example 49 as a solid. ¹H NMR (CDCl₃, 400 MHz) δ 8.71 (d, J=1.6 Hz, 1H), 7.64-7.58 (m, 2H), 7.51-7.47 (m, 3H), 7.36 (d, J=8.4 Hz, 2H), 6.40 (d, J=1.6 Hz, 1H), 5.12-5.11 (m, 1H), 4.53-4.48 (m, 2H), 4.25-4.23 (m, 1H), 4.00-3.96 (m, 1H), 2.50 (s, 3H). MS (ESI) m/z: 401.0 [M+H⁺].

(R)-2-((3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl)isoxazol-3(2H)-one, example 50 was obtained from (R)-2-((3-(4-bromo-3-fluorophenyl)-2-oxooxazolidin-5-yl)methyl)isoxazol-3(2H)-one following the protocol described in step B in the procedure above as a solid. (CDCl₃, 400 MHz) δ 8.56 (d, J=2.4 Hz, 1H), 7.58-7.48 (m, 4H), 7.36-7.34 (m, 3H), 5.98 (d, J=2.4 Hz, 1H), 4.91-5.02 (m, 1H), 4.27-4.20 (m, 3H), 3.90-3.88 (m, 1H), 2.50 (s, 3H). MS (ESI) m/z: 401.1 [M+H⁺].

Example 54 Synthesis of (R)-5-((1H-1,2,3-triazol-1-yl)methyl)-3-(3-fluoro-4-(6-(piperazin-1-yl)pyridin-3-yl)phenyl)oxazolidin-2-one

Step A: Synthesis of (R)-5-((1H-1,2,3-triazol-1-yl)methyl)-3-(4-bromo-3-fluorophenyl)oxazolidin-2-one

2,5-Norbornadiene (13.2 g, 143 mmol) was added to the solution of (R)-5-(azidomethyl)-3-(4-bromo-3-fluorophenyl)oxazolidin-2-one (9.0 g, 28.6 mmol) in Dioxane (200 mL), then the mixture was stirred at 110° C. for 17 hours. Then the reaction mixture was concentrated, and the crude product was purified by column chromatography using silica gel (SiO₂, DCM to DCM:MeOH=95:5) to give (R)-5-((1H-1,2,3-triazol-1-yl)methyl)-3-(4-bromo-3-fluorophenyl)oxazolidin-2-one, as a solid, as well as 2.0 g crude product (<80% purity). MS (ESI) m/z: 382.1, 384.1[M+ACN+H⁺].

Step B: (R)-5-((1H-1,2,3-triazol-1-yl)methyl)-3-(3-fluoro-4-(6-(piperazin-1-yl)pyridin-3-yl)phenyl)oxazolidin-2-one

To a solution of (R)-5-((1H-1,2,3-triazol-1-yl)methyl)-3-(4-bromo-3-fluorophenyl)oxazolidin-2-one (50.0 mg, 0.15 mmol), (6-(piperazin-1-yl)pyridin-3-yl)boronic acid (36.4 mg, 0.18 mmol) and aqueous potassium phosphate tribasic (1M, 0.23 mL, 0.29 mmol) in THF (1 mL) was added 2nd generation xphos precatalyst (5.8 mg, 7.33 μmop under N₂ atmosphere. The mixture was stirred at 60° C. for 16 hours. The mixture was filtered and concentrated to give a residue which was purified by reverse phase prep-HPLC to give (R)-5-((1H-1,2,3-triazol-1-yl)methyl)-3-(3-fluoro-4-(6-(piperazin-1-yl)pyridin-3-yl)phenyl)oxazolidin-2-one, compound 54 as a solid. MS (ESI) m/z: 424.2 [M+H⁺].

The following compound was made using the methods described in Example 54, substituting the appropriate reactants and/or reagents.

Observed Example Structure IUPAC Name (M + H) 55

(5R)-3-[5′- (aminomethyl)-2,2′- difluorobiphenyl-4-yl]-5- (1H-1,2,3-triazol-1- ylmethyl)-1,3- oxazolidin-2-one 386.1

Example 56 Synthesis of (S)-5-(aminomethyl)-3-(3-fluoro-4-(thiophen-2-yl)phenyl)oxazolidin-2-one

To a solution of (S)-5-(aminomethyl)-3-(4-bromo-3-fluorophenyl)oxazolidin-2-one (70.0 mg, 0.24 mmol), tributyl(thiophen-2-yl)stannane (108.0 mg, 0.29 mmol) and potassium phosphate tribasic (0.48 mL, 0.48 mmol) in THF (2 mL) was added 2nd generation xphos precatalyst (19.0 mg, 0.02 mmol) under N₂ atmosphere. The mixture was de-gassed and refilled with N₂ for three times. The reaction mixture was stirred at 60° C. for 16 hours. The reaction mixture was concentrated to give the crude product, which was purified by reverse phase prep-HPLC to give (S)-5-(aminomethyl)-3-(3-fluoro-4-(thiophen-2-yl)phenyl)oxazolidin-2-one, compound 54 as a solid. MS (ESI) m/z: 293.0 [M+H⁺].

Example 57 Synthesis of (S)-4′-(5-((2-aminoacetamido)methyl)-2-oxooxazolidin-3-yl)-2′-fluoro-[1,1′-biphenyl]-4-carboxamide

Step A: Synthesis of (5)-tert-butyl (2-(((3-(4′-carbamoyl-2-fluoro-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl) amino)-2-oxoethyl)carbamate

To a solution of 2-((tert-butoxycarbonyl)amino)acetic acid (35.9 mg, 0.20 mmol) in DMF (1.5 mL) was added DIEA (0.05 mL, 0.27 mmol) and HATU (78.0 mg, 0.20 mmol). The mixture was stirred at 20° C. for 10 minutes then (S)-4′-(5-(aminomethyl)-2-oxooxazolidin-3-yl)-2′-fluoro-[1,1′-biphenyl]-4-carboxamide was added, example 2 (50.0 mg, 0.14 mmol). The resulting mixture was stirred at 20° C. for 16 hours. The reaction mixture was filtered and concentrated to give a residue which was purified by reverse phase prep-HPLC to give (5)-tert-butyl (2-(((3-(4′-carbamoyl-2-fluoro-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl)amino)-2-oxoethyl)carbamate as a solid.

Step B: (S)-4′-(5-((2-aminoacetamido)methyl)-2-oxooxazolidin-3-yl)-2′-fluoro-[1,1′-biphenyl]-4-carboxamide

To a solution of (5)-tert-butyl (2-(((3-(4′-carbamoyl-2-fluoro-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl)amino)-2-oxoethyl)carbamate (70.0 mg, 0.13 mmol) in DCM (5 mL) was added TFA (0.1 mL, 1.30 mmol). The resulting mixture was stirred at 20° C. for 16 hours. The reaction mixture was filtered and concentrated to give a residue which was purified by reverse phase prep-HPLC to give (S)-4′-(5-((2-aminoacetamido)methyl)-2-oxooxazolidin-3-yl)-2′-fluoro-[1,1′-biphenyl]-4-carboxamide, as a solid. MS (ESI) m/z: 386.9 [M+H⁺].

Example 58 Synthesis of (5)-tert-butyl (2-(((3-(4′-carbamoyl-2-fluoro-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl) amino)-2-oxoethyl)carbamate

To a solution of (S)-5-(aminomethyl)-3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)oxazolidin-2-one (50.0 mg, 0.15 mmol) in DMF (2 mL) was added DIEA (0.05 mL, 0.30 mmol) and isocyanatoethane (12.8 mg, 0.18 mmol). The resulting mixture was stirred at 20° C. for 16 hours. The reaction mixture was concentrated to give a residue which was purified by reverse phase prep-HPLC to give (S)-1-ethyl-3-((3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl)urea, compound 56 as a solid. MS (ESI) m/z: 403.9 [M+H⁺].

Example 59 Synthesis of (S)-5-(aminomethyl)-3-(3,5-difluoro-4-morpholinophenyl)oxazolidin-2-one (compound 59)

Step A: Synthesis of 4-(2,6-difluoro-4-nitrophenyl)morpholine

To a solution of 1,2,3-trifluoro-5-nitrobenzene (1.6 g, 8.75 mmol) in DMF (10 mL) was added potassium carbonate (1.3 g, 9.63 mmol) and morpholine (0.8 g, 8.75 mmol) at 20° C. The reaction mixture was stirred at 50° C. for 10 hours. The reaction mixture was poured into EtOAc (50 mL) and washed with brine (50 mL×3). The organic phase was dried over Na₂SO₄, filtered and concentrated to give 4-(2,6-difluoro-4-nitrophenyl) morpholine as a solid. ¹H NMR (CDCl₃, 400 MHz) δ 7.22 (m, 4H), 4.98 (br s, 2H), 3.97 (m, 2H), 3.00 (m, 2H), 1.59 (m, 4H). MS (ESI) m/z: 244.8 [M+H⁺].

Step B: Synthesis of 3,5-difluoro-4-morpholinoaniline

To a solution of 4-(2,6-difluoro-4-nitrophenyl)morpholine (2.3 g, 9.42 mmol) in MeOH (25 mL), was added Pd—C (10% wt, 0.3 g, 2.82 mmol) at 20° C. The reaction was stirred under H₂ balloon at 20° C. for 10 hours. The reaction mixture was filtered and the filtrate was concentrated to give 3,5-difluoro-4-morpholinoaniline as a solid. ¹H NMR (CDCl₃, 400 MHz) δ 6.17 (m, 2H), 3.79 (m, 4H), 3.07 (m, 4H). MS (ESI) m/z: 214.9 [M+H⁺].

Step C: Synthesis of benzyl (3,5-difluoro-4-morpholinophenyl)carbamate

To a solution of 3,5-difluoro-4-morpholinoaniline (1.8 g, 8.40 mmol) in acetone (20 mL) was added benzyl carbonochloridate (2.2 g, 12.60 mmol) at 20° C. followed by a solution of sodium hydrogencarbonate (1.4 g, 16.81 mmol) in water (20 mL). The reaction mixture was stirred at 20° C. for 10 hours, and then was evaporated and dissolved in EtOAc (50 mL). The organic phase was washed with water (50 mL×3), dried over Na₂SO₄, and concentrated to give benzyl (3,5-difluoro-4-morpholinophenyl)carbamate as a solid. ¹H NMR (CDCl₃, 400 MHz) δ 7.37 (m, 7H), 6.96 (d, J=10.4 Hz, 2H), 5.19 (s, 2H), 4.70 (s, 1H), 3.79 (m, 4H), 3.13 (br s, 4H). MS (ESI) m/z: 349.3[M+H⁺].

Step D: Synthesis of (R)-3-(3,5-difluoro-4-morpholinophenyl)-5-(hydroxymethyl)oxazolidin-2-one

To a solution of benzyl (3,5-difluoro-4-morpholinophenyl)carbamate (2.1 g, 6.03 mmol) in THF (30 mL) was added lithium 2-methylpropan-2-olate (1.4 g, 18.09 mmol). The reaction mixture was stirred at 20° C. for 0.5 hours, and then (R)-oxiran-2-ylmethyl butyrate (1.7 g, 12.06 mmol) was added. The resulting mixture was stirred at 20° C. for 10 hours. Solvent was removed and the crude product was purified by column chromatography (SiO₂, EtOAc:PE=2:1) to give (R)-3-(3,5-difluoro-4-morpholinophenyl)-5-(hydroxymethyl)oxazolidin-2-one as a solid. ¹H NMR (CDCl₃, 400 MHz) δ 7.08 (m, 2H), 4.73 (m, 1H), 3.97 (m, 3H), 3.80 (m, 4H), 3.72 (dd, J=3.5, 12.9 Hz, 1H), 3.22 (br s, 2H), 3.13 (br s, 4H). MS (ESI) m/z: 314.9 [M+H⁺].

Step E: Synthesis of (R)-(3-(3,5-difluoro-4-morpholinophenyl)-2-oxooxazolidin-5-yl)methyl methanesulfonate

To a solution of (R)-3-(3,5-difluoro-4-morpholinophenyl)-5-(hydroxymethyl)oxazolidin-2-one (350 mg, 1.11 mmol) in DCM (3 mL) was added methanesulfonyl chloride (191 mg, 1.67 mmol) and triethylamine (225 mg, 2.227 mmol) at 0° C. The reaction mixture was stirred at 23° C. for 10 hours. The mixture was washed with water (20 mL×3). Then the organic phase was dried over Na₂SO₄, filtered and concentrated to give (R)-(3-(3,5-difluoro-4-morpholinophenyl)-2-oxooxazolidin-5-yl)methyl methanesulfonate as a solid. MS (ESI) m/z: 392.9 [M+H⁺].

Step F: Synthesis of (R)-5-(azidomethyl)-3-(3,5-difluoro-4-morpholinophenyl)oxazolidin-2-one

To a solution of (R)-(3-(3,5-difluoro-4-morpholinophenyl)-2-oxooxazolidin-5-yl)methyl methanesulfonate (100.0 mg, 0.26 mmol) in DMF (1 mL) was added sodium azide (21.5 mg, 0.33 mmol). The reaction mixture was stirred at 70° C. for 5 hours. The mixture was diluted with EtOAc (20 mL), washed with brine (15 mL×3). The organic phase was dried over Na₂SO₄, filtered and concentrated to give (R)-5-(azidomethyl)-3-(3,5-difluoro-4-morpholinophenyl)oxazolidin-2-one as an oil. MS (ESI) m/z: 339.9 [M+H⁺].

Step G: Synthesis of (S)-5-(aminomethyl)-3-(3,5-difluoro-4-morpholinophenyl)oxazolidin-2-one

To a solution of (R)-5-(azidomethyl)-3-(3,5-difluoro-4-morpholinophenyl)oxazolidin-2-one (86 mg, 0.23 mmol) in a mixture of THF (2 mL) and water (0.1 mL) was added triphenylphosphine (120 mg, 0.46 mmol). The reaction mixture was stirred at 70° C. for 10 hours. Then the solvent was removed under vacuum, and EtOAc (20 mL) was added to the residue. The organic phase was washed with brine (15 mL×3), dried over Na₂SO₄, filtered and was concentrated to give crude product, which was purified by reverse phase prep-HPLC to give (S)-5-(aminomethyl)-3-(3,5-difluoro-4-morpholinophenyl)oxazolidin-2-one as a solid. ¹H NMR (CDCl₃, 400 MHz) δ 7.22 (m, 2H), 4.2 (t, J=9.2 Hz, 1H), 3.77 (m, 4H), 3.35 (m, 3H), 3.11 (br s, 3H). MS (ESI) m/z: 313.9 [M+H⁺].

Example 60 Synthesis of (S)—N-((3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl)-2,2-dimethylhydrazinecarboxamide (Compound 60)

Step A: Synthesis of (S)—N-((3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl)-1H-midazole-1-carboxamide

To a solution of (S)-5-(aminomethyl)-3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)oxazolidin-2-one (350 mg, 1.05 mmol) in DMF (5 mL) were added DIEA (817 mg, 6.32 mmol) and CDI and the resulting mixture was stirred at 20° C. for 16 hours. The crude was used in next step directly. MS (ESI) m/z: 426.9[M+H⁺].

Step B: Synthesis of (S)—N-((3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl)-2,2-dimethylhydrazinecarboxamide

To a solution of (S)—N-((3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl)-1H-imidazole-1-carboxamide (100 mg, 0.23 mmol) in DMF (2 mL) was added 1,1-dimethylhydrazine (85 mg, 1.41 mmol) and the resulting mixture was stirred at 40° C. for 12 hours. The reaction mixture was evaporated to dryness and the crude product was purified by reverse phase Prep-HPLC to give (S)—N-((3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl)-2,2 dimethylhydrazinecarboxamide as a solid. MS (ESI) m/z: 441.0 [M+Na⁺].

Example 62 Synthesis of (S)-methyl ((3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl)carbamate (compound 62)

To a solution of (S)-5-(aminomethyl)-3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)oxazolidin-2-one in DMF (2 mL) was added DIEA (0.08 mL, 0.451 mmol) and methyl carbonochloridate under N₂ atmosphere. The resulting mixture was de-gassed and refilled with N₂ for three times. The reaction mixture was stirred at 15° C. for 16 hours, then was diluted with water (5 mL) and extracted with EtOAc (10 mL×3). The organic layer was dried over Na₂SO₄, filtered and concentrated to give the crude product, which was purified by reverse phase Prep-HPLC to give (S)-methyl ((3-(2-fluoro-4′-(methylthio)-[1,1′-biphenyl]-4-yl)-2-oxooxazolidin-5-yl)methyl)carbamate as a solid. LC/MS: MS (ESI) m/z: 391.1 [M+H⁺]

The following compound was made using the methods described in Example 62, substituting the appropriate reactants and/or reagents.

Example Structure IUPAC Name (M + H) 63

ethyl ({(5S)-3-[2-fluoro-4′- (methylsulfanyl)biphenyl-4- yl]-2-oxo-1,3-oxazolidin-5- yl}methyl)carbamate 405.0

Example 64 Synthesis of (5R)-5-((1H-1,2,3-triazol-1-yl)methyl)-3-(2-fluoro-4′-(S-methylsulfonimidoyl)-[1,1′-biphenyl]-4-yl)oxazolidin-2-one (compound 64)

To a solution of (5R)-5-((1H-1,2,3-triazol-1-yl)methyl)-3-(2-fluoro-4′-(methylsulfinyl)-[1,1′-biphenyl]-4-yl)oxazolidin-2-one (40.0 mg, 0.10 mmol) (generally prepared using the procedure of example 54) and sodium azide (9.7 mg, 0.15 mmol) in CHCl₃ (2 mL) was added H₂SO₄ (1 μl, 0.02 mmol). The mixture was stirred at 45° C. for 5 hours. The mixture was quenched with saturated Na₂CO₃ (1 mL). The mixture was concentrated and purified by reverse phase Prep-HPLC to give (5R)-5-((1H-1,2,3-triazol-1-yl)methyl)-3-(2-fluoro-4′-(S-methylsulfonimidoyl)[1,1′-biphenyl]-4-yl)oxazolidin-2-one as a solid. ¹H NMR (400 MHz, CD₃OD) δ 8.40 (s, 1H), 8.25 (d, J=8.4 Hz, 2H), 8.14 (s, 1H), 8.00 (d, J=7.9 Hz, 2H), 7.69-7.59 (m, 2H), 7.42 (d, J=7.9 Hz, 1H), 5.25 (br s., 1H), 5.10-5.00 (m, 2H), 4.38 (t, J=8.9 Hz, 1H), 4.08 (dd, J=5.3, 8.6 Hz, 1H), 3.93 (s, 3H). MS (ESI) m/z: 416.2 [M+H⁺].

Example 65 Biological Assays

Mycobacterium tuberculosis (Mtb) Growth Assay

Inhibition of Mycobacterium tuberculosis (Mtb) growth was assessed on two in vivo-relevant carbon sources, glucose and cholesterol, at pH 6.8. For glucose as a carbon source, the media consisted of Middlebrook 7H9 broth supplemented with 4 g/L glucose, 0.08 g/L NaCl, 5 g/L BSA fraction V and 0.05% tyloxapol. For cholesterol as a carbon source, the media consisted of Middlebrook 7H9 broth supplemented with 97 mg/L cholesterol, 0.08 g/L NaCl, 5 g/L BSA fraction V and 0.05% tyloxapol. Mtb expressing green fluorescent protein (Mtb-GFP; H37Rv pMSP12::GFP) was pre-adapted to growth on the relevant carbon source in Middlebrook 7H9-broth base supplemented with bovine serum albumin and tyloxapol prior to the screen. Bacteria were dispensed into 384-well microtiter plates at approximately 2×10⁴ actively growing cells in 24 μL volumes per well. Microtiter plates were pre-dispensed with 0.2 μL compound, dimethylsulfoxide (negative control) or rifampicin (25 μM; positive control). Cells were exposed to 2-fold serial dilutions of compounds from 50 μM to 0.049 μM. In some experiments, compounds were tested at lower concentrations. Growth inhibition was assessed after a 7-day growth period by measuring fluorescence using a spectrophotometer. In negative control wells, cells were still actively growing at the time of readout. The lowest concentration of test compound required to inhibit 95% of the growth of the bacteria was defined as the MITC95. All studies were done in a BSL3 facility.

Staphylococcus aureus Growth Assay

Inhibition of Staphylococcus aureus (methicillin resistant, MB5393, COL) growth was assessed in cation adjusted Mueller Hinton II broth (CAMHB) in 384-well microtiter plates. Bacteria were dispensed into microtiter plates at approximately 5×10⁵ actively growing cells in 49 μL volumes per well. Cells were exposed to 2-fold serial dilutions of compounds from 200 μM to 0.195 μM and growth compared to drug-free control. Compound dilutions were prepared in 100% dimethylsulfoxide and added to microtiter plates in 1 μL volumes per well. Full growth control wells contained dimethylsufoxide and bacteria. No growth control wells contained dimethysulfoxide and CAMHB but no bacteria. Growth inhibition was assessed after a 22-hour growth period by measuring optical density using a spectrophotometer. The lowest concentration of test compound required to inhibit 95% of the growth of the bacteria was defined as the MITC95. All studies were done in a BSL2 facility.

Mitochondrial Protein Synthesis Assay

Inhibition of mitochondrial protein synthesis was assessed in HepG2 cells by comparing the levels of two subunits of oxidative phosphorylation enzyme complexes, subunit I of Complex IV (COX-I) and the 70 kDa subunit of Complex II (SDH-A). COX-I is mitochondrial DNA encoded and SDH-A is nuclear DNA encoded. HepG2 cells were seeded in 96-well collagen coated plates at 8,000 cells per well and exposed to 2-fold serial dilutions of compounds from 100 μM to 6.25 μM. Microtiter plates were incubated for approximately 5 replication cycles (4 days) prior to assessment of protein levels using a kit as described by the manufacturer (ab110217 MitoBiogenesis In Cell ELISA Kit, Abcam, Cambridge, Mass.). Inhibition of mitochondrial protein synthesis was expressed as a ratio of COX-1 to SDH-A levels.

Mycobacterium tuberculosis (Mtb) Growth Assay

Inhibition of Mycobacterium tuberculosis (Mtb) growth was assessed on two in vivo-relevant carbon sources, glucose and cholesterol, at pH 6.8. For glucose as a carbon source, the media consisted of Middlebrook 7H9 broth supplemented with 4 g/L glucose, 0.08 g/L NaCl, 5 g/L BSA fraction V and 0.05% tyloxapol. For cholesterol as a carbon source, the media consisted of Middlebrook 7H9 broth supplemented with 97 mg/L cholesterol, 0.08 g/L NaCl, 5 g/L BSA fraction V and 0.05% tyloxapol. Mtb expressing green fluorescent protein (Mtb-GFP; H37Rv pMSP12::GFP) was pre-adapted to growth on the relevant carbon source in Middlebrook 7H9-broth base supplemented with bovine serum albumin and tyloxapol prior to the screen. Bacteria were dispensed into 384-well microtiter plates at approximately 2×10⁴ actively growing cells in 24 μL volumes per well. Microtiter plates were pre-dispensed with 0.2 μL compound, dimethylsulfoxide (negative control) or rifampicin (25 μM; positive control). Cells were exposed to 2-fold serial dilutions of compounds from 50 μM to 0.049 μM. In some experiments, compounds were tested at lower concentrations. Growth inhibition was assessed after a 7-day growth period by measuring fluorescence using a spectrophotometer. In negative control wells, cells were still actively growing at the time of readout. The lowest concentration of test compound required to inhibit 95% of the growth of the bacteria was defined as the MITC95. All studies were done in a BSL3 facility.

Staphylococcus aureus Growth Assay

Inhibition of Staphylococcus aureus (methicillin resistant, MB5393, COL) growth was assessed in cation adjusted Mueller Hinton II broth (CAMHB) in 384-well microtiter plates. Bacteria were dispensed into microtiter plates at approximately 5×10⁵ actively growing cells in 49 μL volumes per well. Cells were exposed to 2-fold serial dilutions of compounds from 200 μM to 0.195 μM and growth compared to drug-free control. Compound dilutions were prepared in 100% dimethylsulfoxide and added to microtiter plates in 1 μL volumes per well. Full growth control wells contained dimethylsufoxide and bacteria. No growth control wells contained dimethysulfoxide and CAMHB but no bacteria. Growth inhibition was assessed after a 22-hour growth period by measuring optical density using a spectrophotometer. The lowest concentration of test compound required to inhibit 95% of the growth of the bacteria was defined as the MITC95. All studies were done in a BSL2 facility.

Mitochondrial Protein Synthesis Assay

Inhibition of mitochondrial protein synthesis was assessed in HepG2 cells by comparing the levels of two subunits of oxidative phosphorylation enzyme complexes, subunit I of Complex IV (COX-I) and the 70 kDa subunit of Complex II (SDH-A). COX-I is mitochondrial DNA encoded and SDH-A is nuclear DNA encoded. HepG2 cells were seeded in 96-well collagen coated plates at 8,000 cells per well and exposed to 2-fold serial dilutions of compounds from 100 μM to 6.25 μM. Microtiter plates were incubated for approximately 5 replication cycles (4 days) prior to assessment of protein levels using a kit as described by the manufacturer (ab110217 MitoBiogenesis In Cell ELISA Kit, Abcam, Cambridge, Mass.). Inhibition of mitochondrial protein synthesis was expressed as a ratio of COX-1 to SDH-A levels.

Mtb Cho Mtb Glu MRSA COL MPS Example MITC95_μM MITC95_μM MITC95 μM IC50_μM 1 0.03 0.04 25 12.2 2 0.03 0.02 200 >25 3 0.78 1.14 100 >20 4 0.09 0.04 200 22 5 0.09 0.04 200 >20 6 0.04 0.04 100 >20 7 0.09 0.04 200 >20 8 0.04 0.04 200 >20 9 0.14 0.09 200 >20 10 0.09 0.09 200 >20 11 0.14 25.1 200 NA 12 1.14 1.14 200 NA 13 0.19 0.19 200 >20 14 1.14 0.78 200 NA 15 0.58 1.14 200 NA 16 0.39 0.19 200 >20 17 0.29 0.09 200 >20 18 0.09 0.04 50 >20 19 0.09 0.485 200 >20 20 0.58 0.14 200 >20 21 1.5 0.39 200 25 22 0.19 0.04 100 >20 23 0.19 0.19 200 >20 24 0.09 0.04 200 >20 25 0.19 0.04 200 >20 26 1.5 0.78 200 >20 27 0.78 0.39 200 >50 28 1.14 0.3 200 >100 29 1.5 0.39 200 >25 30 0.39 0.09 200 >20 31 0.78 0.39 200 >20 32 0.29 0.24 200 >20 33 0.19 0.845 200 >20 34 0.04 0.04 200 >20 35 0.58 1.14 200 NA 36 0.48 1.5 200 NA 37 0.39 0.29 200 >20 38 0.39 0.14 200 >20 39 0.78 0.585 200 >20 40 0.09 0.076 4.688 >15 41 0.04 0.04 200 8 42 1.5 1.5 200 >20 43 0.19 0.58 200 >20 44 0.04 0.19 200 >20 45 0.39 1.14 200 NA 46 0.29 0.585 200 >20 47 0.01 0.03 0.7813 >20 48 0.78 0.39 200 >100 49 0.58 0.58 200 >20 50 0.58 0.29 200 >20 54 0.215 0.24 2.34 >20 55 0.19 0.19 50 >20 56 0.39 0.39 100 >20 57 0.535 0.29 25 50 58 0.19 0.58 200 >20 59 0.39 0.09 200 >20 60 1.14 2.3 200 NA 62 0.04 0.04 200 10 63 0.19 0.29 200 18 64 0.09 0.09 0.39 >20 linezolid 3.14 4.58 6.25 8 

What is claimed is:
 1. A compound of formula I

or a pharmaceutically acceptable salt thereof, wherein: R¹ is —CH₂N(R²)₂, —CH₂NR²COR³, —CH₂NR²COOR³, —CH₂NR²CON(R²)₂, —CH₂NR²CONR²N(R²)₂, —CH₂NR²SO₂R³, —CON(R²)₂, —C═NOR³, —CH₂OR⁴, —CH₂NR²R⁴, or —CH₂R⁶. each occurrence of R² is independently selected from H, C₁-C₆ alkyl, C₂-C₆ alkenyl, and C₃-C₆ cycloalkyl, wherein said C₁-C₆ alkyl, said C₂-C₆ alkenyl, and said C₃-C₆ cycloalkyl can be optionally substituted with up to four substituents, which are independently selected from halogen, —OCH₃, —OH, —NH₂, —NHCH₃, and —N(CH₃)₂; R³ is H, C₁-C₆ alkyl, C₂-C₆ alkenyl, and C₃-C₆ cycloalkyl, wherein said C₁-C₆ alkyl, said C₂-C₆ alkenyl and said C₃-C₆ cycloalkyl can be optionally substituted with up to four substituents, which are independently selected from halogen, —OCH₃, —OH, —NH₂, —NHCH₃, and —N(CH₃)₂; R⁴ is a 5- or 6-membered heterocycle, which is optionally substituted with R⁵; R⁵ is selected from H, halogen, C₁-C₆ alkyl, C₃-C₆ alkenyl, and C₃-C₆ cycloalkyl, wherein said C₁-C₆ alkyl, said C₃-C₆ alkenyl, and said C₃-C₆ cycloalkyl can be optionally substituted with up to four substitutents, which are independently selected from halogen, —OCH₃, —OH, —NH₂, —NHCH₃, and —N(CH₃)₂; R⁶ is H, C₁-C₆ alkyl, or a 5-membered heterocycle, wherein said 5-membered heterocycle is optionally substituted with up to two R⁷; each occurrence of R⁷ is H, halogen, oxo, C₁-C₆ alkyl, C₂-C₆ alkenyl, or C₃-C₆ cycloalkyl, wherein said C₁-C₆ alkyl and said C₃-C₆ cycloalkyl can be optionally substituted with from one to four substituents which are independently selected from halogen, —OCH₃, —OH, —NH₂, —NHCH₃, and —N(CH₃)₂; E is a 6-membered aryl or a 5- or 6-membered heteroaryl containing from one to three heteroatoms independently selected from S, O, and N, wherein said aryl and said heteroaryl are optionally substituted with up to four substituents, which are independently selected from halogen, —CN, —CF₃, —CHF₂, —CH₂NH₂, —CH₂NHCOCH₃, —OCF₃, —OCHF₂, —OH, —O—(C₁-C₆)alkyl, C₁-C₆ alkyl, and C₃-C₆ cycloalkyl; A is a heterocycle optionally substituted with up to four R⁸, or an aryl optionally substituted with up to four R⁸; each occurrence of R⁸ is independently selected from H, halogen, C₁-C₆ alkyl, C₃-C₆ cycloalkyl, C₃-C₆ heterocycloalkyl, benzyl, —OCF₃, —OCHF₂, —OR³, ═O, —CN, —NO₂, —SR³, —SF₅, —SCF₃, —SOR³, —SO₂R³, —S(═O)(═NH)R², —N(R²)₂, —NR²COR³, —SO₂N(R²)₂, —NR²SO₂R³, —COOH, —COOR³, —CON(R²)₂, and —C(R⁹)₂N(R²)₂, wherein said C₁-C₆ alkyl, C₃-C₆ cycloalkyl, C₃-C₆ heterocycloalkyl, and benzyl are optionally substituted with up to four F, —OCH₃, —OH, ═O, NH₂, NHCH₃, and N(CH₃)₂; and each occurrence of R⁹ is independently selected from H, C₁-C₆ alkyl, and C₃-C₆ cycloalkyl.
 2. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein: R¹ is —CH₂OR⁴ or —CH₂NR²R⁴; and R⁴ is selected from:


3. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein R¹ is CH₂R⁶ and R⁶ is selected from:


4. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein A is:

wherein R⁸ represents up to four optional ring carbon substituents, which can be the same or different.
 5. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein A is:

wherein: m=is 0, 1, 2, or 3; each occurrence of R⁸ is independently selected from H, halogen, C₁-C₆ alkyl, C₃-C₆ cycloalkyl, C₃-C₆ heterocycloalkyl, benzyl, —OCF₃, —OCHF₂, —OR³, ═O, —CN, —NO₂, —SR³, —SF₅, —SCF₃, —SOR³, —SO₂R³, —S(═O)(═NH)R², —N(R²)₂, —NR²COR³, —SO₂N(R²)₂, —NR²SO₂R³, —COOH, —COR⁹, —COOR³, —CON(R²)₂, and —C(R⁹)₂N(R²)₂, wherein said C₁-C₆ alkyl, C₃-C₆ cycloalkyl, C₃-C₆ heterocycloalkyl, and benzyl are optionally substituted with up to four F, —OCH₃, —OH, ═O, NH₂, NHCH₃, and N(CH₃)₂; R¹⁰ is selected from H, C₁-C₆ alkyl and C₃-C₆ cycloalkyl, wherein said C₁-C₆ alkyl and said C₃-C₆ cycloalkyl are optionally substituted with from one to four substituents, which are independently selected from F, —OCH₃, —OH, NH₂, NHCH₃, and N(CH₃)₂; R¹¹ is selected from H, C₁-C₆ alkyl and C₃-C₆ cycloalkyl, —COR⁹, —COOR⁵, —CON(R⁹)₂, and —SO₂R⁹; each occurrence of R¹² is independently selected from H, halogen, C₁-C₆ alkyl, C₃-C₆ cycloalkyl, benzyl, —OCF₃, —OCHF₂, —OR³, —CN, —NO₂, —SR³, —SF₅, —SCF₃, —SOR³, —SO₂R³, —S(═O)(═NH)R², —N(R²)₂, —NR²COR³, —SO₂N(R²)₂, —NR²SO₂R³, —COOH, —COR⁹, —COOR³, —CON(R²)₂, and —C(R⁹)₂N(R²)₂, wherein said C₁-C₆ alkyl, C₃-C₆ cycloalkyl, and benzyl are optionally substituted with up to four F, —OCH₃, —OH, NH₂, NHCH₃, and N(CH₃)₂; R¹¹ is selected from H, halogen, C₁-C₆ alkyl, C₃-C₆ cycloalkyl, benzyl, —OCF₃, —OCHF₂, —OR³, —CN, —NO₂, —SR³, —SF₅, —SCF₃, —SOR³, —SO₂R³, —S(═O)(═NH)R², —N(R²)₂, —NR²COR³, —SO₂N(R²)₂, —NR²SO₂R³, —COOH, —COR⁹, —COOR³, —CON(R²)₂, and —C(R⁹)₂N(R²)₂, wherein said C₁-C₆ alkyl, C₃-C₆ cycloalkyl, and benzyl are optionally substituted with up to four F, —OCH₃, —OH, NH₂, NHCH₃, and N(CH₃)₂; and W is selected from O, S, SO, SO₂, and S(═O)(═NH); and and wherein

represents a double or a single bond.
 6. The compound of claim 4, or a pharmaceutically acceptable salt thereof, having the formula:

wherein: R¹ is —CH₂NH₂, —CH₂NHC(O)CH₃, —CH₂NHC(O)—C₃-C₆cycloalkyl, or CH₂R⁶.
 7. The compound of claim 6, or a pharmaceutically acceptable salt thereof, wherein R¹ is —CH₂NH₂.
 8. The compound of claim 6, or a pharmaceutically acceptable salt thereof, wherein A is:

wherein R⁸ represents up to four optional ring carbon substituents, which can be the same or different.
 9. The compound of claim 1, or a pharmaceutically acceptable salt thereof, having the structure:


10. The compound of claim 9, or a pharmaceutically acceptable salt thereof, having the structure:


11. A pharmaceutical composition which comprises a therapeutically effective amount of a compound according to claim 1, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.
 12. A method for treating a bacterial infection which comprises administering to a subject in need of such treatment (i) a therapeutically effective amount of a compound according to claim 1, or a pharmaceutically acceptable salt thereof.
 13. The method of claim 12, wherein the bacterial infection is due to Mycobacterium tuberculosis.
 14. The method according to claim 12, wherein the compound or the pharmaceutically acceptable salt thereof is administered orally, parentally, or topically.
 15. The method according to claim 13, wherein the M. tuberculosis is a drug resistant mycobacterial strain.
 16. The method according to claim 13, further comprising the step of administering a second therapeutic agent for treating M. tuberculosis.
 17. The method of claim 16, wherein the second therapeutic agent is selected from the group consisting of: ethambutol, pyrazinamide, isoniazid, levofloxacin, moxifloxacin, gatifloxacin, ofloxacin, kanamycin, amikacin, capreomycin, streptomycin, ethionamide, prothionamide, cycloserine, terididone, para-aminosalicylic acid, clofazimine, clarithromycin, amoxicillin-clavulanate, thiacetazone, meropenem-clavulanate, and thioridazine.
 18. (canceled) 